The federal government’s top ethics official has taken the unusual step of sending a letter to the Environmental Protection Agency questioning a series of actions by Administrator Scott Pruitt and asking the agency to take “appropriate actions to address any violations.”

The letter, sent to Kevin Minoli, the E.P.A. official designated as the agency’s top ethics official, addresses questions about Mr. Pruitt’s rental for $50 a night of a condominium linked to an energy lobbyist, as well as his government-funded flights to his home state of Oklahoma. The letter also cites reporting last week in The New York Times that agency staff members who raised concerns about these and other actions found themselves transferred or demoted.

“The success of our government depends on maintaining the trust of the people we serve,” said David J. Apol, acting director of the Office of Government Ethics, in the letter sent Monday morning to the E.P.A. “The American public needs to have confidence that ethics violations, as well as the appearance of ethics violations, are investigated and appropriately addressed.”

The letter walks through the three areas of concern. The first is related to the Capitol Hill condo Mr. Pruitt rented early last year from the wife of an energy lobbyist whose firm had business matters before the E.P.A.

Mr. Apol noted that Mr. Pruitt did not apparently seek advice about the appropriateness of the deal until after he had moved out. Then, the agency ethics officer who was asked to evaluate the matter, which took place this month following news reports about the lease, was given “limited information” about the deal, and wasn’t informed, for example, that Mr. Pruitt’s daughter also used the condo.

“Additional information has now come to light that calls into question whether the earlier determination that the administrator paid market value for the use he made of the apartment would still be valid,” Mr. Apol’s letter says.

The trips home to Oklahoma, on flights paid by the government, also concerned Mr. Apol, who said that they “do raise concerns about whether the administrator is using his public office for personal gain in violation of ethics rules.” Mr. Apol noted there were also news reports that an E.P.A. staff member had been asked to help Mr. Pruitt find an apartment in Washington, which also might have violated rules.

Most disturbing, Mr. Apol said, were the reports in The Times that agency staff may have been punished after raising concerns about Mr. Pruitt’s actions.

“If true, it is hard to imagine any action that could more effectively undermine an agency’s integrity than punishing or marginalizing employees who strive to ensure compliance with the laws and regulations that safeguard that integrity,” the letter says.

The Office of Government Ethics does not have the power to punish Mr. Pruitt or to demand that he respond to the letter. But as the chief ethics officer for the executive branch of the federal government, Mr. Apol’s point of view has clout and he can ask that President Trump take action to punish a federal official who has violated federal rules.