In an unprecedented move since Mr. Trump resumed power, government workers appeared to be resisting, at least temporarily, an unexpected maneuver in their complex interaction with the world’s wealthiest individual. The whirlwind of events—contradictory tweets from Mr. Musk, remarks from the President, and messages from agency leaders—left many feeling perplexed.

Following Mr. Musk’s email, several agencies swiftly communicated to their employees that they were not compelled to provide the requested five bullet points about their activities.

The Department of Health and Human Services clarified in an email, stating, “There is no expectation for H.H.S. employees to respond to O.P.M., and choosing not to reply will have no bearing on your employment with the agency.”

Moreover, the agency advised those who wished to respond to “consider that what you write could be seen by malicious foreign entities and tailor your response accordingly.”

Simultaneously, during a meeting with French President Emmanuel Macron, Mr. Trump praised Mr. Musk’s demand as “genius,” asserting that those who chose not to respond would be “semi-fired” or outright “fired.”

Late Monday, Mr. Musk added another layer to the situation on his social media platform.

He mentioned, “Subject to the President’s discretion, they will receive another opportunity,” evidently directing this at federal employees who failed to reply by the original deadline. “A second failure to respond will lead to termination.”

He further claimed, “The email request was incredibly simple — merely type a few words and hit send! Yet so many could not even accomplish that basic task, sometimes encouraged by their supervisors. Have you ever seen such INCOMPETENCE and DISREGARD for how YOUR TAX DOLLARS are being utilized?”

Until this past weekend, high-ranking officials in Mr. Trump’s administration largely supported Mr. Musk’s vision of a leaner, more efficient government, free from what Republicans argue is “woke” ideology. Numerous employees have faced termination or suspension, and entire agencies, such as the U.S. Agency for International Development, have been significantly scaled back. Remote workers have also been instructed to return to offices or risk losing their jobs.

However, the reactions to Musk’s recent email suggest there may be limits to how far he, as the head of the newly established Department of Government Efficiency, can go in influencing the federal bureaucracy.

The Musk email sparked alarm about jurisdiction and security among various federal agencies. It created a divide within Mr. Trump’s cabinet, with some leaders mandating compliance while others advised their staff to disregard the demands.

Chiefs of staff and personnel directors at national security and intelligence agencies spent the weekend coordinating a consistent response, according to a senior U.S. official familiar with the conversations. This effort began when Kash Patel, Mr. Trump’s recently appointed F.B.I. director, instructed the bureau’s staff to “pause any responses” to Musk’s directive.

According to the official, who wished to remain anonymous to discuss internal matters, there was concern that Mr. Musk might react negatively over the weekend on social media. The developments stirred frustration among cabinet secretaries and agency heads towards Musk for his interference.

Many agency leaders expressed discontent with the notion that an outsider was attempting to override their personnel protocols. Others worried that employees could disclose sensitive or classified information in their replies to Musk.

In the C.I.A., although no public statement was released, agency staff were discreetly instructed not to reply to Musk’s email, hoping the situation would resolve itself, according to a source with knowledge of the internal decision.

Officials at the White House denied any reduction in Mr. Musk’s influence or any discord among the President’s key advisors.

“Everyone is collaborating as a unified team at the direction of President Trump,” stated White House Press Secretary Karoline Leavitt. “Any suggestion to the contrary is entirely false.”

A senior White House official, who spoke on the condition of anonymity due to internal discussions, noted that the rapidly evolving plans by Mr. Musk and the Department of Government Efficiency were “exactly the point,” even if they caused some tension within the administration.

However, the conflicting directives left many of the nation’s 2.3 million federal employees unclear about their necessary actions—even after the Office of Personnel Management reassured them on Monday.

While television broadcasts displayed Mr. Trump praising Mr. Musk, the personnel department informed agencies that responding to the Musk email was now “voluntary,” and not replying would not equate to resignation, contrary to Mr. Musk’s implication.

Such dissent among Mr. Trump’s top officials is unusual for a president whose requests for unwavering loyalty have spurred dramatic executive actions from his team, all working cohesively to advance his agenda swiftly.

Over the weekend, a number of high-ranking officials defied Mr. Musk, guiding their employees to “pause” or “not respond” to the request for five specific activities they performed the previous week. Employees from the Departments of State, Defense, Energy, Homeland Security, and Justice were clearly instructed not to comply.

“For the time being, D.O.E. employees are requested to pause any direct communications regarding the O.P.M. email,” wrote Energy Secretary Chris Wright in a weekend update. A senior official from the State Department asserted, “No employee is required to disclose their activities outside of the established departmental channels.”

Meanwhile, the President’s chosen leaders at the Treasury, General Services Administration, Department of Transportation, and Office of Management and Budget directed their employees to adhere to Musk’s recent command. An email from the Treasury stated, “You are instructed to respond to this message before the deadline,” emphasizing that “we anticipate compliance will not pose any difficulties or take much time.”

This divide among advisors comes just two days ahead of Mr. Trump’s first full cabinet meeting of his second term scheduled for Wednesday. Eight years prior, his inaugural cabinet gathering became an event of enthusiastic praise for the President as aides expressed their appreciation for working under him, with one remarking it was a “blessing.”

Such a scenario could still unfold again on Wednesday, as members of Mr. Trump’s current circle have consistently lauded him in recent weeks. Following a meeting with Russian officials last week, Secretary of State Marco Rubio repeatedly emphasized that “Trump is the only leader capable of achieving peace in Ukraine.”

This article was co-reported by Madeleine Ngo and Nicholas Nehamas from Washington.