Three of the NFL's top health and safety officers confronted the National Institutes of Health last June after the NIH selected a Boston University researcher to lead a major study on football and brain disease, Outside the Lines has learned.

The new information contradicts denials by the NFL and a foundation it partners with that the league had any involvement or input in the fate of a $16 million study to find methods to diagnose -- in living patients -- chronic traumatic encephalopathy, a brain disease found in dozens of deceased NFL players.

Outside the Lines reported in December that the NFL, which in 2012 promised an "unrestricted" $30 million gift to the NIH for brain research, backed out of funding the new study over concerns about the lead researcher, Boston University's Dr. Robert Stern, who has been critical of the league. In the story, a senior NIH official said that the NFL retained veto power over projects it might fund with its donation, and it effectively used that power in the Stern study. Almost immediately, NFL spokesman Brian McCarthy deemed the report "inaccurate." The league and the foundation both said the league's overall donation comes with no strings attached.

But Dr. Walter Koroshetz, director of the National Institute for Neurological Disorders and Stroke, told Outside the Lines this week that the NFL raised several concerns about Stern's selection during a June conference call that included Jeff Miller, the NFL's senior vice president for health and safety; Dr. Richard Ellenbogen, co-chairman of the Head, Neck and Spine Committee; and Dr. Mitch Berger, chairman of the sub-committee on the long-term effects of brain and spine injury.

The NFL alleged that the review process that led to Stern's selection was marred by conflicts of interest, Koroshetz said. In addition, league officials charged that Stern was biased because he had filed an affidavit opposing the settlement of a lawsuit in which thousands of former players accused the NFL of hiding the link between football and brain damage.

"It was a fairly clear message that they transmitted," said Koroshetz, who was on the call with representatives of the Foundation for the NIH, a nonprofit organization independent of the NIH that administers the NFL grant.

An NIH advisory council concluded unanimously in September that there was no basis to the NFL's claims, Koroshetz said. He called the selection of Stern's group "highly meritorious."

Ultimately, the NIH decided to use taxpayer money to fund the study, Koroshetz said, because the research is so important and there was no indication that the NFL -- which had trumpeted the project in its own health and safety report -- was still willing to pay for it.

When asked about the new information on Wednesday, the Foundation for the NIH acknowledged that "NFL scientific advisers raised a concern to the FNIH about potential conflict of interest and bias." The foundation "flagged this concern to the NIH," the statement said, under the terms of an agreement between the two organizations that governs the handling of the league's $30 million donation.

The agreement states that the FNIH "will use reasonable efforts to facilitate any donor-related issues that arise" on any NFL-funded research project.

The NFL declined to address questions about the concerns it raised to the NIH. In a statement Wednesday, Miller said the "NIH made the decision to move forward with the BU study with its own funds and to use NFL funds" for another CTE project.

"The NFL has no veto power as part of its $30 million grant to the FNIH," Miller said. "We recognize NIH has final approval on its funding decisions."

After the Outside the Lines report in December, four Congressional Democrats from the House Energy and Commerce Committee requested information from the NIH and the FNIH, expressing concern that the NFL may have tried to influence "the selection of NIH research applicants." The NIH and the FNIH have said they are working to fulfill that request.

Robert Stern, director of clinical research for Boston University's Alzheimer's Disease and CTE centers, has a complicated history with the NFL. Stephan Savoia/AP Images

"These revelations fly in the face of the NFL's assertions that their contributions for CTE and head trauma research had 'no strings attached,'" said U.S. Rep. Jackie Speier, a California Democrat who sits on the House Armed Services' Subcommittee on Oversight and Investigations, in a statement. Speier was not part of the original group to request information but became interested because of broader implications of the science, according to a spokesman.

"If this money does have strings, then the NFL needs to own up to the fact that it's attempting to control the science," Speier said. "I'm deeply troubled by the conduct of the NFL, and I also question the arrangement where a 'nonprofit' arm of the NIH accepts corporate donations in a way that enables researchers to be bullied by corporate interests."

Despite the league's multiple public contentions that its $30 million award was unrestricted, FNIH financial statements describe it as a "conditional contribution" that allows the NFL to cancel its funding. The league can offer input on "research concepts" through a "stakeholder board" that allows league representatives to discuss projects with the NIH's scientific leadership, according to a Memorandum of Understanding between the FNIH and NIH, released under the Freedom of Information Act.

According to Koroshetz, NFL officials signed off on the $16 million study before the NIH issued a request for applications on July 29, 2014. Two months earlier, the White House announced the NFL's support for the long-term study during a "concussion summit" convened by President Obama.

But Koroshetz said the league raised its objections shortly after the completion of a two-stage review process. One of the objections, he said, concerned a potential conflict of interest during the first stage, in which about a dozen experts grade the grant applications.

The NFL asserted that at least one reviewer had a professional relationship with Dr. Ann McKee, a neuropathologist affiliated with Boston University and the Department of Veterans Affairs. McKee is listed as an investigator on the Stern-led study, examining the "mechanisms" of CTE. But Koroshetz said the reviewer had worked with McKee on an opinion article, not scientific research, which is not a violation of NIH conflict-of-interest rules.

Berger, who leads the department of neurological surgery at the University of California San Francisco, has previously accused McKee and Boston University of scientific bias, charging that "their whole existence, their funding, relies on this [idea] they're perpetuating that it's a fact if you play football you're going to have some form of cognitive impairment."

McKee, who has been critical of the NFL, received a $6 million grant in 2013 through the NFL's $30 million donation to the NIH. But, according to Koroshetz, the NFL raised objections about Stern because of the 61-page affidavit he filed in opposition to the settlement of the concussion suit.

Stern, who said he was not paid to submit the opinion, wrote that the settlement would not adequately compensate some of the most severely disabled players.

The advisory council ruled that Stern's history was not evidence of scientific bias, Koroshetz said.

Koroshetz said it wasn't until December -- seven months after the NIH notified Stern that his group had won the grant, and after the funding cycle had ended -- that the FNIH indicated verbally that the NFL might pay for part of the study, but it was "never definitive." By then the NIH had committed to funding the project on its own.

Miller said in his statement Wednesday that NFL funds will be used for a longitudinal study on CTE in the future. Koroshetz told Outside the Lines that no determination has been made yet about future studies.