WASHINGTON — In making an end run around Congress to appoint Anthony J. Tata, a retired brigadier general with a history of Islamophobic and other inflammatory views, to a top Defense Department post, President Trump has once again put the military exactly where it does not want to be: in the middle of a political battle that could hurt bipartisan support for the Pentagon.

Mr. Tata, who had been nominated to the No. 3 job at the Pentagon, was unlikely to win Senate approval because of past incendiary comments, according to congressional staff members from both sides of the aisle. At a time when vulnerable Republican senators are grappling with how to deal with the movement to end systemic racism that has rolled across the country, Mr. Tata’s nomination to the top policy post was widely seen as a step too far. Senator James M. Inhofe, Republican of Oklahoma, canceled Mr. Tata’s confirmation hearing last Thursday just 30 minutes before it was set to begin.

But on Sunday, the White House sidestepped Congress. Mr. Trump had Defense Secretary Mark T. Esper appoint Mr. Tata to a temporary senior position in the same Defense Department office. Arcane rules say that if he stays in that office for 90 days, Mr. Tata can then take the original job in an acting capacity — without Senate approval. (Mr. Tata had withdrawn his name from consideration for that job on Sunday, and Mr. Trump formally withdrew the nomination on Monday.)

On Monday at the Pentagon, where military officials have already been engaged in a tug of war with Mr. Trump over the president’s insistence that the military continue to honor former Confederate leaders, the Tata maneuver was greeted with both resignation and consternation.

“This is only going to exacerbate civil-military tensions and is an added insult to the policy team in the Pentagon, which has already been hollowed out,” said Derek Chollet, a former assistant secretary of defense in the Obama administration. “And the idea of having a voice like his at the highest levels of the Pentagon during a moment of such tension and turmoil, both of which will only get worse in the coming months, is very alarming.”

Mr. Tata endeared himself to the president using a tried-and-true method: praising Mr. Trump on Fox News and bashing his political opponents. Mr. Tata promoted conspiracy theories that John O. Brennan, the C.I.A. director under President Barack Obama, wanted to oust Mr. Trump from office, even through assassination if necessary.

Mr. Tata also said Mr. Obama and Michelle Obama, the first lady, engaged in “borderline treasonous” behavior by expressing their dismay over a Trump presidency during the transition period.

Mr. Tata’s views, expressed in a series of tweets, struck a jarring note. He called Islam “the most oppressive violent religion” and referred to Mr. Obama as a “terrorist leader.” He has since apologized for the remarks, which were first reported by CNN.

“At a moment when the Defense Department is warning about the dangers of politicization and trying to keep its personnel out of the 2020 presidential campaign, Tata’s appointment demonstrates that apolitical orders only mean so much,” said John Gans, a Pentagon speechwriter for former Defense Secretary Ashton B. Carter. “Tata’s blowtorch tweets set a horrible example and precedent with three months to go in a contentious campaign.”

After the comments caught the public’s attention, several senior retired military officers dropped their support for Mr. Tata. Gen. Joseph L. Votel, the former head of the Central Command; Gen. Tony Thomas, the former head of the Special Operations Command; and Lt. Gen. David A. Deptula, a former top Air Force general, all asked in June that their names be removed from a letter backing Mr. Tata’s nomination sent by 36 current and former leaders to the Armed Services Committee.

Mr. Tata was meant to succeed John C. Rood, who resigned in February at Mr. Trump’s request. Mr. Rood had pushed back on efforts to withhold military aid to Ukraine, a central issue in Mr. Trump’s impeachment hearings.

One Republican on the armed services panel, Senator Kevin Cramer of North Dakota, had publicly indicated that he was prepared to block the nomination over an unrelated Pentagon policy on adding names to the Vietnam Veterans Memorial. Other Republican lawmakers were privately unsettled by Mr. Tata’s inflammatory remarks, and taking a vote on the nomination would have put four Republicans on the panel, who are facing difficult re-election battles, in a particularly unsavory position: Senators Joni Ernst of Iowa, Martha McSally of Arizona, Thom Tillis of North Carolina and David Perdue of Georgia.

Democratic lawmakers on the panel were united in opposing Mr. Tata, making the threat of Mr. Cramer’s opposition potentially fatal to moving the nomination out of the committee. That was enough for Mr. Inhofe to cancel the hearing.

The night before canceling the hearing, Mr. Inhofe was overheard discussing the matter in a phone call with Mr. Trump. The call was overheard because Mr. Inhofe put it on speakerphone to hear better as he sat in the Trattoria Alberto restaurant in Washington. During the conversation, Mr. Trump suggested he might give Mr. Tata a different appointment.

On Monday, Mr. Inhofe indicated he would not try to stand in the way of Mr. Trump’s latest move. “While I have always stressed the need to have Senate-confirmed leadership in top Pentagon positions, I believe it is within the president’s authority to appoint D.O.D. officials when and as appropriate,” Mr. Inhofe said in an emailed response to a request for comment. “These are clearly critical positions within the department where a full bench is needed.”

Eric Schmitt contributed reporting.