Two top officers of the United Paperworkers International Union "voluntarily" took paid leaves of absence yesterday while fighting federal charges that they embezzled $360,000 in union funds.

A spokesman announced that the two men indicted July 19 by a Brooklyn grand jury - Joseph P. Tonelli, president and Henry Segal, secretary-treasurer of the 300,000 member AFL CIO union - agreed to step aside during a specially called meeting of the paperworkers' 17-member executive board at the Sheraton Park Hotel.

Tonelli and Segal have denied the charges, but a source close to the union said the two men "bowed to the inevitable" by temporarily leaving their jobs before being forced to do so."

Two union area vice-presidents, Wayne Gleen of Little Rock and Nicholas Vrataric of Ann Arbor, Mich., were elected as temporary replacements.

Vrataric, the new secretary-treasurer, said in a telephone interview that the executive board called the emergency session "because all of us were disturbed about the image the indictments placed on the union."

"We were exploring various alternatives and decided the easiest way out for everyone was to approach them [Tonelli and Segal] to see whether they would consider stepping aside voluntarily . . . It was made clear we were unhappy about the situation."

Some $50,000 of the embezzled union funds, according to the grand jury indictment, went to two Atlanta lawyers to intercede with Justice Department officials.

Federal prosecutors are continuing an investigation to determine whether anyone obstructed justice with those attempts to intercede, sources said.