Senate Republicans are pushing back against President Trump Donald John TrumpBiden says voters should choose who nominates Supreme Court justice Trump, Biden will not shake hands at first debate due to COVID-19 Pelosi: Trump Supreme Court pick 'threatens' Affordable Care Act MORE’s controversial clemency for three servicemen accused of war crimes, saying it sets a bad precedent and undermines the military justice system.

The president’s intervention was opposed by senior military leaders, who warned that disrupting the chain of command could erode discipline.

Even one of Trump’s staunchest supporters — Sen. Lindsey Graham Lindsey Olin GrahamHarris slams Trump's Supreme Court pick as an attempt to 'destroy the Affordable Care Act' Sunday shows preview: Lawmakers prepare for SCOTUS confirmation hearings before election Confirmation hearing for Trump's Supreme Court pick to start Oct. 12 MORE (R-S.C.), a retired Air Force judge advocate general — said Trump’s actions risk harming the Defense Department’s legal mechanisms.

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“I am concerned that the system will feel intimidated and that if you intervene too early and too often that it’s going to have a chilling effect,” Graham said Tuesday. “Good order and discipline can only be maintained if there’s consequences to misconduct.”

Graham added that he would “give a lot of weight” to those within the military who thought the service members’ actions “went out of bounds.”

Sen. Susan Collins Susan Margaret CollinsSenate GOP set to vote on Trump's Supreme Court pick before election Democratic senator to party: 'A little message discipline wouldn't kill us' Poll: 57 percent of Americans think next president, Senate should fill Ginsburg vacancy MORE (R-Maine), a member of the Senate Appropriations Defense Subcommittee, on Tuesday said, “I do not believe the president should intervene in the military criminal justice system.”

Sen. Lisa Murkowski Lisa Ann MurkowskiSenate GOP set to vote on Trump's Supreme Court pick before election Supreme Court fight pushes Senate toward brink Democratic senator to party: 'A little message discipline wouldn't kill us' MORE (R-Alaska), a fellow subcommittee member, said, “It did cause concern for me.”

“What I read, I was concerned,” Murkowski added. “There is a chain of command there, and typically that is adhered to.”

Sen. Mitt Romney Willard (Mitt) Mitt RomneyCrenshaw looms large as Democrats look to flip Texas House seat The Hill's Morning Report - Sponsored by Facebook - Republicans lawmakers rebuke Trump on election Trump dumbfounds GOP with latest unforced error MORE (R-Utah) advised that Trump should listen to senior military commanders when assessing such difficult situations.

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“I do believe that the weight of experience that would be provided by military advisers should be given preeminence in a matter of that nature,” he said.

Trump’s intervention last month halted disciplinary action against three service members: Navy SEAL Eddie Gallagher, who was convicted of posing for a photo with the corpse of an ISIS fighter but acquitted of murder; Army Maj. Mathew Golsteyn, who was awaiting trial after he admitted to killing a suspected bombmaker in Afghanistan after his capture and release; and former Army Lt. Clint Lorance, who was sentenced to 19 years in prison for the second-degree murder of two Afghan civilians.

Trump’s actions were opposed by former Navy Secretary Richard Spencer and Army Secretary Ryan McCarthyRyan McCarthyOvernight Defense: Trump's battle with Pentagon poses risks in November | Lawmakers launch Fort Hood probe | Military members can't opt out of tax deferral Lawmakers launch investigation into Fort Hood after 28th death this year Overnight Defense: China aims to double nuclear arsenal | Fort Hood commander removed after string of deaths MORE.

Trump declared on Twitter on Nov. 21 that Gallagher would not lose his prestigious Trident pin, signifying his membership in the SEALs.

Rear Adm. Collin Green, who accepted command of the Navy’s special warfare program in September of 2018 and said he wanted to restore “good order and discipline” to the elite SEAL program after a series of scandals, had pushed for Gallagher to be stripped of his Trident pin.

“This case was handled very badly from the beginning. Get back to business!” Trump tweeted last month.

The president at times has complained about the military’s rules of engagement, calling them too narrow.

“We train our boys to be killing machines, then prosecute them when they kill!” Trump tweeted in October, when he announced he would review the Golsteyn’s case. His murder trial had been scheduled to begin this month.

Graham, who is also a member of the Senate Appropriations Defense Subcommittee, said Tuesday he understood Trump’s concern about narrow rules of engagement but warned that maintaining discipline on the battlefield is critical.

“I think the president believes that the rules of engagement were not clear, that we put our folks in a bad spot. I have some sympathy for that, but having been a military lawyer most of my adult life, the one thing you’ve got to maintain in a war is a well-disciplined force,” he said. “You can’t have people becoming the judge and jury on the battlefield.”

Sen. Joni Ernst Joni Kay ErnstOn The Trail: Making sense of this week's polling tsunami Tillis appears to reinforce question about COVID-19 death toll The power of incumbency: How Trump is using the Oval Office to win reelection MORE (R-Iowa), who joined the U.S. Army Reserves after graduating from college and served as a company commander in Kuwait and Iraq, borrowed Green’s language when asked about Trump’s pardons.

“I just think we need good order and discipline,” she said.

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Sen. Thom Tillis Thomas (Thom) Roland TillisNetflix distances from author's comments about Muslim Uyghurs but defends project Overnight Energy: Trump officials finalize plan to open up protected areas of Tongass to logging | Feds say offshore testing for oil can proceed despite drilling moratorium | Dems question EPA's postponement of inequality training On The Trail: Making sense of this week's polling tsunami MORE (R-N.C.), a member of the Senate Armed Services Committee, said Trump’s pardons give “pause” because they represent presidential intervention on an almost granular level.

“I don’t know what circumstances led him to do it, but any time you get into that level of command you always give pause because you’ve got to always preserve that command component,” he said.

Spencer characterized Trump’s action on Gallagher as “a shocking and unprecedented intervention in a low-level review” in a Washington Post opinion piece published Nov. 27.

“It was also a reminder that the president has very little understanding of what it means to be in the military, to fight ethically or to be governed by a uniform set of rules and practices,” he wrote.

The Pentagon has said Spencer was fired for trying to work out a deal with Trump behind Esper’s back that would have allowed Gallagher to keep his Trident.

Democrats say the whole incident shows that Trump’s decisionmaking process needs closer scrutiny.

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Sens. Patrick Leahy (D-Vt.) and Sheldon Whitehouse (D-R.I.) asked the Justice Department in a letter last week whether the Office of the Pardon Attorney was involved in the decisions regarding Gallagher, Golsteyn and Lorance.

Leahy and Whitehouse noted in their letter the “pardons were issued in the face of strong opposition from senior military officials, who warned that such pardons would undermine the U.S. military justice system and shake faith in our military’s commitment to abide by the laws of war.”

Sen. Jack Reed John (Jack) Francis ReedOvernight Defense: Appeals court revives House lawsuit against military funding for border wall | Dems push for limits on transferring military gear to police | Lawmakers ask for IG probe into Pentagon's use of COVID-19 funds Democrats push to limit transfer of military-grade gear to police When 'Buy American' and common sense collide MORE (D-R.I.), the ranking member of the Armed Services Committee, used his opening statement at an unrelated hearing Tuesday to voice his displeasure at Trump’s intervention.

“The president has the power to pardon, but he has a responsibility to use that power wisely, not recklessly,” Reed said, speaking directly to the service secretaries and chiefs, adding that Trump’s “disregard for our military justice system risks undermining the confidence of our service members in the rule of law and their chain of command.”

Reed later told The Hill that an Armed Services Committee hearing on the matter would be “very useful.”

“We can’t ignore it,” he said.

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Some Senate Republicans either defended Trump or declined to criticize him.

Armed Services Committee Chairman James Inhofe James (Jim) Mountain InhofeOvernight Defense: Appeals court revives House lawsuit against military funding for border wall | Dems push for limits on transferring military gear to police | Lawmakers ask for IG probe into Pentagon's use of COVID-19 funds Democrats push to limit transfer of military-grade gear to police Chamber of Commerce endorses McSally for reelection MORE (R-Okla.), a staunch Trump ally, said Trump’s intervention in the military justice cases and Spencer’s firing “really didn’t” trouble him.

“The president made some statements that I’d have made in a different way, but that’s his prerogative and that’s how he sees his job,” Inhofe said Tuesday.

Senate Majority Leader Mitch McConnell Addison (Mitch) Mitchell McConnellHawley warns Schumer to steer clear of Catholic-based criticisms of Barrett Senate GOP set to vote on Trump's Supreme Court pick before election Harris slams Trump's Supreme Court pick as an attempt to 'destroy the Affordable Care Act' MORE (R-Ky.) declined to comment Tuesday when asked about the issue at a press conference.

Updated Dec. 6 at 10:24 a.m.