Senior officials deny such a change is in the works, despite guidance shared with agents around the country in recent days.

Federal agents around the country were told in recent days that the F.B.I. would no longer investigate confrontations with immigration agents — cases that sometimes yield evidence that could be used to prosecute Department of Homeland Security agents implicated in violent encounters, according to people briefed on the decision.

If enacted, such a change would sharply limit law enforcement scrutiny of immigration agents, as the Trump administration draws mounting criticism over killings at the hands of federal officers. In the last two weeks, two fatal shootings by Immigration and Customs Enforcement agents in Texas and Maine have thrust the government’s tactics back into the spotlight.

F.B.I. managers around the country received a written notice informing them of the change on Thursday, according to the people familiar with the matter who spoke on the condition of anonymity to describe internal communications. The same day, some ICE agents around the country were notified by their F.B.I. counterparts.

The guidance shared with them said that the bureau would stop investigating claims of assaults against Department of Homeland Security agents, the people said. Even though such investigations are intended to determine whether the officers were in fact attacked, they can provide a crucial means of gathering evidence implicating the agents themselves.

A joint statement by the Justice Department and the Department of Homeland Security, however, denied that any such change was underway.

“The relationship between D.H.S. and D.O.J. in investigating assault on federal officer cases has not changed, and F.B.I. will continue to investigate in accordance with agency policy,” the statement said. “This administration has been clear, anyone who assaults law enforcement will be prosecuted to the fullest extent of the law.”