Story highlights Top officials at the Phoenix VA deny any existence of a secret waiting list

The retired physician who brought the allegations to light says they are lying

Members of Congress have called for hearings on the Phoenix VA

The top officials at the Phoenix VA denied any existence of a secret waiting list in an in-depth interview with CNN on Tuesday, and they denied that delays in care caused the deaths of U.S. veterans at the facility.

But only hours after making these denials, the top VA physician who first appeared on CNN and brought the allegations to light declared that the VA officials are lying and that they are covering up what has happened in Phoenix.

Several other off-record sources inside the Phoenix VA agreed with Dr. Sam Foote.

Sources told CNN the managers at the VA concocted an elaborate scheme to cover up long wait times there. The sources said more than 1,400 vets were placed on the purported secret list and that documents were shredded to hide the evidence. According to sources, at least 40 U.S veterans died waiting for care at the facility, many of whom were on the list.

These issues raised in CNN's exclusive investigation have quickly drawn attention in Washington.

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On Monday, President Barack Obama stated he has called for an investigation into what has happened in Phoenix.

"The moment we heard about the allegations around these 40 individuals who had died in Phoenix, I immediately ordered the secretary of Veterans Affairs, Gen. (Eric) Shinseki , to investigate," he said.

In recent days, numerous members of Congress have called for hearings on the Phoenix VA. At least three members of Congress have publicly called for the resignation of Sharon Helman, the Phoenix VA director.

VA leaders: We've never ordered a secret list

But in an interview with CNN on Tuesday, Helman and her chief of staff, Dr. Darren Deering, denied any secret effort to cover up or hide wait times.

"We have never instructed our staff to create a secret list, to maintain a secret list, to shred a secret list -- that has never come from our office as far as instruction to our staff," said Deering.

"It's never come from me," added Helman.

Only hours later, watching Helman and Deering make those statements to CNN, Foote shook his head in disbelief.

"Are you kidding?" asked Foote incredulously.

The 24-year VA physician and clinic director, who recently retired and went public with the details of the list, went on the air publicly for the first time with CNN one week ago.

"They started this secret list in February of 2013," Foote continued. "At some time, they changed over from paper to electronic, in early summer, maybe approximately June or July. And transferred names over to the electronic waiting list. And she [Helman] was called on an ethics consult evaluation about that -- it's written down, documented in July."

The e-mails Foote referred to were reported by CNN in its original Phoenix VA story last week. The e-mails from July 2013 show that top management, including Helman, were well-aware about the actual wait times, knew about the off-the-books list and even defended its use to her staff.

In one internal Phoenix VA e-mail, dated July 3, 2013, one staffer raises concerns about the secret electronic list and that officials are praising its use:

"I have to say, I think it's unfair to call any of this a success when Veterans are waiting 6 weeks on an electronic waiting list before they're called to schedule their first PCP appointment," the e-mail states. "Sure, when their appointment is created, it's can be 14 days out, but we're making them wait 6-20 weeks to create that appointment."

The e-mail adds: "That is unethical and a disservice to our Veterans."

Repeated requests for interview denied

For nearly three weeks, CNN had been requesting an interview with Helman, asking her to respond to the allegations about the secret wait list and the charge that more than 40 U.S. veterans died waiting for medical care from her facility.

CNN's requests were repeatedly denied. On Monday, a team from CNN Investigations tried to ask Helman questions as she walked out of the VA building in the parking lot.

The director had parked in an "emergency vehicles only" space outside the facility's ER entrance. She left the building surrounded by armed police who held the CNN team back. She climbed into her Mercedes sports coupe and drove off without saying a word.

But barely an hour after that parking lot rebuff, aides to Helman called and offered an on-camera interview with her.

In the interview Tuesday morning, the Phoenix VA director admitted that veterans on the waiting list did die, but she said she did not know any names of those veterans who had died waiting for care. She said the question of whether veterans had died waiting for care are now being investigated by the VA Inspector General's Office.

"Those are the allegations that we've asked the office of inspector general to review," Helman stated.

Helman and Deering were pressed about whether they had direct knowledge about allegations of document shredding and a secret list.

"Again those allegations are ones that the office of Inspector General are reviewing right now. When we heard about this during the House Veterans Affairs Committee, is the first time we have heard about those allegations, and that is why we asked the Office of Inspector General to come in and do a thorough and impartial review," Helman said.

The hearing to which she referred was held on April 9.

However, the Office of the Inspector General has been investigating the Phoenix VA since the fall of 2013, when it first learned allegations of secret lists and the 40 deaths in September.

Foote's warnings to the Inspector General

Last year and earlier this year, Foote sent letters to officials at the VA Office of the Inspector General. His letters contained details about the secret electronic waiting list and about the large number of veterans who died waiting for care, many hidden on the secret list.

As a result of Foote's letters, inspectors went to Phoenix and have been actively pursuing allegations that Helman and her staff did have a secret list specifically created to hide that veterans had been waiting up to 21 months for care.

Multiple sources inside the Phoenix VA tell CNN that under direction of management, evidence of the list was shredded and that at least 40 veterans, some of whom were on that list and waiting for care, died before getting an appointment. Those sources say Helman and Deering knew about it because it was their plan.

Foote and several other sources inside the Phoenix VA confirmed to CNN that inspectors have interviewed them about these allegations months ago.

On Tuesday, despite insisting she just recently learned of the allegations, Helman did admit that inspectors interviewed her in December.

"They don't tell us what the allegations are surrounding their investigation," said Helman. "I can just confirm that yes, they were here in December."

When asked directly whether evidence of wait times was shredded and whether the secret list existed, Deering stated:

"I think there is some confusion amongst our staff. When we came on as a leadership team in 2012, the practice at that time was that they would schedule new veterans who would were coming in for care way out into the future. Sometimes a year, sometimes 14 months. And that was the appointment that that veteran was given.

"As we started to tackle our challenges of access, we implemented a tool that the VA uses nationally called the electronic wait list. And what that tool is it's an electronic waiting list that allows us to everyday look to see who is waiting for an appointment.

"So what we did is we took those patients that were scheduled way out into the future, and we put them on this national tool that the VA uses so that we could track them. What that did is, rather than having an appointment 14 months out into the future, it put them on this EWL electronic waiting list, so that when we had an appointment that came open, so if a veteran called next week and canceled their appointment, we could pull a veteran off this list and get them into that slot.

"So it actually improved the probability of these veterans getting an appointment sooner. And in that transition time, I think there was some confusion among staff, I think there were some folks who did not understand that, and I think that's where these allegations are coming from.

"But like Miss Helman said, we take them very seriously and that is why we have invited the office of inspector general to come in and do an investigation: A thorough and unbiased investigation and get to the bottom of this. And we look forward to their report."

Director: I share the same concerns of my staff

Helman was asked about the numerous sources -- some in tears -- who have told CNN that patients have died waiting on these lists and the wait list and the wait times were being hidden from the overseers in Washington or the region.

"What we are saying is that we implemented the electronic wait list, and any concerns that staff have, I share in those same concerns," Helman said. "And that is why we've asked the Office of Inspector General to come in and look at that."

Asked whether VA officials have found cases where veterans were on the waiting list and have died, Deering said:

"Yes, and that is, um, in the course of health care delivery we have patients who unfortunately pass away. We have found veterans on the list who have died, but we have not been able to connect their death to the delay in getting their care."

When CNN asked again whether Helman knew about 40 veterans who died while waiting for care at the Phoenix VA, she stated:

"I think that's a question for the Office of Inspector General. They came in December and did a site review, and they were here last week, so I believe that's a question for them."

Foote, along with several sources inside the VA, say there is no confusion. They say the secret list existed and veterans died.

Asked whether he was backing down from his allegations, Foote said, "no sir."

When Foote was asked whether what Helman and Deering said was false, Foote said, "I would say so, yes."

When asked whether he still believes that 40 or more U.S. veterans died waiting for care at the Phoenix VA, Foote stated said, "That number may be as high as 45 now."

And when asked again what he thought about Helman and Deering stating there was no secret waiting list and that no one shredded any evidence of a waiting list, Foote said, "I don't believe that's true."

CNN has spoken with several other sources inside the VA, who agree with Foote that Helman and Deering are not telling the truth.

No plans to resign

Helman, reminded that Obama has asked for an investigation and that three member of Congress have asked for her resignation, indicated she plans to stay put.

"I tell you right now the office of Inspector General is here and reviewing all of the allegations, and as the leader of this organization, I am going to continue to provide the best health care that these veterans deserve and have earned. "

Regarding the details about the electronic wait list, Deering added: "We use an electronic system in the VA health system for our records for our appointment system. Previously, those appointments were scheduled in the electronic database out into the future, our scheduling database."

Deering further addressed why appointments were scheduled so far out into the future:

"Because that's when we had availability two years ago. ... And now it's 55 days. And that improvement over the last two years is the result of assigning resources, we have hired more physicians and nurses and clerks and expanded our clinic times on weekends and evenings. We've expanded out infrastructure. We've opened a new 60,000 square feet clinic in the south side of the valley. We are continuing to expand to meet those demands."

After the Inspector General team went to Phoenix in December, the investigation seemed to have stalled, until Foote went public with his interview last week.

Foote and others have openly wondered whether officials in upper VA management might have or could have held back the investigation until it was such big news it had to move ahead again.

CNN has also learned the investigation may now be expanding and that it is no longer looking just at veterans who died waiting for initial care but also is looking into veterans who died waiting for return care or follow-up appointments that they could not get.