Former Patriots doctor Thomas Gill, right, watches as offensive linemen Chris Barket and Nate Soder go through some workouts before a game in December 2013. (Boston Globe/Boston Globe via Getty Images)

The NFL Players Association, in a court document recently filed in an unrelated case, alleged that a team physician for the New England Patriots altered the medical treatment of a player in an effort to bolster a legal case that would force the player to return his signing bonus to the team.

A grievance letter sent by the players’ union cites an e-mail from former team physician Thomas Gill that the NFLPA contends shows Gill telling Patriots owner Robert Kraft and President Jonathan Kraft that he was “trying to put together a case” that would compel former defensive end Jonathan Fanene to return $3.85 million after he suffered a knee injury in 2012. The letter further asserts that Patriots Coach Bill Belichick directed Gill to delay any surgery on Fanene’s knee while an effort was made to persuade the player to retire, thus forgoing his bonus.

Reached by telephone Thursday, Gill called the grievance a “legal maneuver” and insisted he put the player’s health ahead of the organization’s concerns. The Patriots did not respond to multiple requests seeking comment.

The substance of the grievance provides a window into the potential conflicts of interest and competing pressures that result when physicians employed by teams provide primary care to players. The Collective Bargaining Agreement between NFL owners and players stipulates that a team physician’s primary obligation in providing care “shall be not to the club but instead to the player-patient.”

However, difficult judgments about drugs, procedures and treatment are further complicated when the best course of treatment clashes with the best interests of the team.

Fanene was released by the Patriots in August 2012 for “failure to disclose physical condition,” a claim that if proved would have allowed the team to recoup a signing bonus.

The players’ union sent the letter to the NFL management council on June 19, 2013, demanding that the Patriots terminate Gill in accordance with the terms of the CBA.

Fanene’s agent, Angelo Wright, confirmed the e-mails cited in the NFLPA letter were subpoenaed in a labor dispute between Fanene and the team. Wright said Fanene accepted a settlement agreement from the Patriots that bars him from discussing the matter. It also prevents Fanene from pursuing a civil case against either the Patriots or Gill.

The confidential letter entered the public record last week, when the NFL’s lawyers included it as an exhibit in an unrelated case concerning the conduct of NFL physicians. In urging U.S. District Court judge William Alsup to dismiss a class action lawsuit in which more than 1,300 former players allege that NFL medical staffs regularly violate laws in plying their teams with addictive narcotics to mask injuries, the NFL argued that the CBA between owners and players provides a grievance process to resolve legal-medical disputes and attached the letter as evidence of that process. The e-mails cited in the grievance letter were not included in the court filing.

In April 2014, the Patriots announced Gill had stepped down as the team physician. Gill claimed his resignation had nothing to do with the grievance.

NFLPA President DeMaurice Smith said he couldn’t discuss the details of the grievance, the related hearing or the terms of the eventual settlement but did express concern over the Patriots’ internal communication cited in the letter.

“It makes serious allegations about the integrity and independence of a team doctor providing medical care to a player,” Smith said. “The allegations would suggest behavior that is completely inappropriate. I will look forward to seeing what the league intends to do as far as investigating this pursuant to their personal conduct policy.”

Gill said Thursday: “Guys always know that they are treated as a patient and not as a player, and that’s always something that I was very proud of during my tenure.”

Gill acknowledged Fanene passed a team physical before signing a three-year contract with the Patriots on March 20, 2012, after spending seven seasons with the Cincinnati Bengals. According to the Boston Globe, Fanene also passed a second team physical in training camp and did well in a handful of early practices before his release in late August 2012.

“It just didn’t work out,” Belichick told reporters at the time. “Nothing to add other than that. It just didn’t work out.”

The Patriots later sought to reclaim Fanene’s bonus money on the grounds that he had arthritis in his left knee and failed to disclose that he needed pain medications to practice and play.

Gill confirmed he wrote an e-mail to Kraft using the phrase “trying to put together a case,” but he disputed the context.

He said the training staff asked him to summarize for the Patriots’ owners why the player had been cut so soon after receiving a signing bonus.

“If it was an e-mail to Mr. Kraft, it was basically saying, ‘I’m going to put together the chronology the training staff had asked me to put together,’ ” he said.

In its grievance letter, the players’ union alleged that Gill initially scheduled Fanene for arthroscopic surgery to treat a knee injury. However, he subsequently “took the direction of Head Coach Bill Belichick” to “play four corner offense” (a metaphorical reference to a stalling tactic in basketball) and delay any surgery, and “ultimately Dr. Gill refused to do the surgery at all,” advising Fanene that if he wanted the surgery, he should use his personal physician.

Gill also confirmed receiving such direction in an e-mail from Belichick but said he was unclear on what Belichick meant.

“Coach Belichick sent an e-mail that said something about ‘let’s play some four corners here,’ which I think had to do with the timing,” Gill said. “It’s vague to me at this point. . . .

“He was saying let’s slow this process down till we can figure out what’s going on with Jonathan. Coach was talking about a day or two of trying to figure things out.”

He said the directive “had zero effect” on his treatment of Fanene. “There was never any care withheld or anything like that.”

In the grievance letter, the union also alleged “there is evidence that Dr. Gill may have fabricated and/or back-dated notes of certain meetings in an effort to advance the Patriots legal case against Mr. Fanene,” but no supportive evidence was included in its letter.

Wright said he had never seen a team so brazenly seek the release of a player. “Not to that degree,” the agent said. “It depends on the fish, I guess. Depends on what they’re fishing for.”

Gill served as team physician for several New England professional sports teams and was involved in some controversies involving high-profile players.

Patriots tight end Rob Gronkowski, for example, reportedly clashed with the doctor over treatment of a forearm injury that prematurely ended Gronkowski’s 2012 season and then required four surgeries to properly heal.

Gill also served as the medical director for the Boston Red Sox from 2005 to 2011 and drew the ire of Jacoby Ellsbury for misdiagnosing four fractured ribs that limited the outfielder to 18 games in 2010.

Following the 2011 season, the Red Sox eliminated the position of medical director, effectively severing ties with Gill.

Gill also served as team physician for the Boston Bruins from 1998 to 2012 and the New England Revolution of MLS from 1998 to 2010.

Upon his departure from the Patriots last year, the team issued a statement saying, “We greatly appreciate the many years of dedicated service and innovation that Dr. Gill provided our team and wish him well in the future.”

Fanene, now 32, never returned to the NFL.