Gov. Andrew M. Cuomo’s hiring practices are under investigation, as F.B.I. agents and federal prosecutors have begun examining how staff members working in the governor’s office are being paid by other New York State authorities and agencies.

The governor’s office received a “document subpoena” months ago, according to Richard Azzopardi, a Cuomo spokesman. “We have cooperated, providing necessary documents,” he said.

Mr. Azzopardi called the line of inquiry “absurd.”

“The agencies are all part of the same executive branch, and this administration follows the exact same lawful hiring process we inherited from previous administrations stretching back decades,” he said. “If there are questions about it, call George Pataki,” referring to the three-term former Republican governor.

The F.B.I. inquiry was first reported by The Times-Union in Albany, which said that agents had interviewed “a number of people” who work in the governor’s office, even though their salaries are carried on the budgets of other state agencies and authorities.