(CNN) Appointment wait times at the Department of Veterans Affairs are not getting better.

Despite billions of extra dollars poured into the agency in the last year and numerous reforms intended to improve veterans' access to care, whistleblowers and internal documents obtained by CNN reveal some VA facilities continue to grapple with appointment wait times of months or more.

Even at the Phoenix VA medical center, where CNN learned last year "secret" appointment lists were hiding how veterans were dying waiting for care, sources say complicated wait-time calculations obscure ongoing appointment delays.

"The reality is veterans are waiting months -- three, six months at a time, sometimes more -- for care at the Phoenix VA," said one source in Phoenix who agreed to speak to CNN anonymously because of fears of retaliation.

The source said this includes veterans waiting for potentially critical health procedures, such as colonoscopies, and other categories of specialty care that require timely attention.

In August, more than 8,000 requests for care had wait times longer than 90 days at the Phoenix VA, according to documents obtained by CNN, but whistleblowers say delays like these are not accurately reflected in public data because of changes in the VA's method of measuring wait times.

"The VA central office enables an official line that's not consistent with reality," the source in Phoenix said.

Additional VA documents show ongoing delays in care are not limited to Phoenix.

An internal VA draft memo from August warns, "Currently wait times are increasing significantly," referring to an overall increase of appointments with delays.

VA Deputy Secretary Sloan Gibson, who received this internal memo, told CNN there are almost 500,000 appointments with extended wait times, which includes appointments with delays longer than 30 days and veterans waiting on a list for appointments to become available.

According to Gibson, the number of appointments with extended waits is even higher than it was more than a year ago, when government and media reports revealed veterans were dying while waiting for care in the midst of an immense backlog of appointments.

"How can it be?" Gibson said. "The lesson that we've seen in location after location is when we improve access to care, whether it's by adding staff or space or productivity or care in the community, more veterans come to VA for more care."

Gibson said since the 2014 scandal, the VA has created twice the capacity that should be needed to meet health care needs of veterans enrolled in the system, yet he said the increased capacity has increased demand.

He added that each month the VA completes about 1 million appointments on the same day veterans want to be seen, but he admits there are still some waiting too long for care.

"The challenge that we have is a structural challenge," he said. "We work every single day trying to find ways to make it better."

Gibson serves at the right hand of VA Secretary Bob McDonald, who took the helm of the agency and began implementing reforms after an internal audit found inappropriate scheduling practices were "systemic" at VA facilities in 2014, which was followed by the resignation of former Secretary Eric Shinseki.

McDonald has overseen the implementation of $15 billion in extra funding Congress approved for the VA to improve veterans' access to health care, and in August, McDonald said the VA is completing appointments in less than a week on average.

Yet whistleblowers on the ground at some VA facilities tell CNN the average wait times publicly reported by the VA do not reflect the experiences of veterans.

For example, at the Los Angeles VA medical center -- the largest in the nation -- public data released by the VA states the average wait time was less than four days for completed mental health appointments in August.

An internal document obtained by CNN says the average wait time for new patients seeking mental health care at the LA VA was 43 days in August, however.

"They've started to measure the numbers differently more than they have actually improved the patients actual wait time in many cases," said a source in Los Angeles.

The VA has publicly confirmed a change in wait-time calculations.

Previously, wait times were measured by tracking the time that elapsed from the day an appointment was created until the day it was completed.

Now, the VA calculates wait times by measuring the time between the date a patient prefers to be seen and the date the appointment is actually completed.

When asked if the VA implemented the calculation change to conceal health care delays, Gibson said, "I wouldn't stand for it, not for a minute."

Gibson said the new measurement allows VA officials to more accurately assess how effectively the VA is meeting veterans' preferences as well as their clinical needs.

He added that he believes accountability of senior VA officials, which he personally oversees, is essential to transforming the VA's culture, but he said about half the senior leaders in the VA's health department have turned over in the last two years, so many of those who oversaw inappropriate scheduling practices exposed in last year's scandal are now gone.

Gibson would not cite a specific number of people who were disciplined specifically for issues related to the scandal, but he said, "I never ever saw an organization where leadership and management excellence was defined by how many people you fire."

According to a congressional source, the VA has fired three lower-level staffers for wait-time manipulations, while three senior VA leaders were removed through the Veterans Access, Choice and Accountability Act, a 2014 law that expedited the VA process for firing executives. Five other VA executives recommended for removal through the 2014 law either resigned or retired.

Dr. Katherine Mitchell, who disclosed information about delays in care at the Phoenix VA to Congress and CNN last year, said many of the VA administrators who retaliated against whistleblowers during the 2014 scandal remain in top positions.

"The culture of retaliation continues," Mitchell said. "At this point in the VA, you risk your job, you risk your reputation if you speak up for patient care problems. You do not risk your job if you retaliate against someone. And it should be just the reverse."

A VA inspector general report released in October exposed how delayed treatment in the Phoenix VA's urology department significantly affected the care of patients who became sick or, in some cases, died in recent years.

Mitchell said the problems continue, adding that she has "no hesitation" patients are still dying while waiting for care.

"Right now no one knows how many appointments are delayed or for how long they're delayed," Mitchell said. "I would question any statistic that comes out of the VA."