WASHINGTON — A former Secret Service agent, with a background investigating the Gambino crime family, is serving as the chief of security for Scott Pruitt, the administrator of the Environmental Protection Agency, and has helped build an unusual and costly protective apparatus around him.

The agent, Pasquale Perrotta, has clashed — at least once physically — with top E.P.A. officials who challenged Mr. Pruitt’s spending, and has steered at least one E.P.A. security contract to a business associate, according to interviews with current and former senior agency officials.

Officially, Mr. Perrotta leads Mr. Pruitt’s protective detail, but he plays a far larger role at the E.P.A., offering security justifications for management, personnel and spending decisions, said the officials, who were not authorized to speak publicly and feared retribution. Mr. Perrotta’s outsize influence has placed him at the center of inquiries by the E.P.A. inspector general’s office into excessive spending and possible violations of contracting rules by Mr. Pruitt’s administration, according to the senior officials.

When Mr. Pruitt and his team became convinced that his office might have been bugged by environmentalists or disgruntled career employees, Mr. Perrotta recommended that a sweep for surveillance devices be conducted by a company owned by Edwin Steinmetz, who is listed as a vice president at a security firm Mr. Perrotta operates on the side, the senior officials said. Mr. Perrotta also used agency funds to hire Italy-based private security guards to protect Mr. Pruitt during a trip to Italy, they said.