About 25 FBI agents were withdrawn tonight from the border of the Red Lake Indian Reservation, where they had been sent after a law enforcement center was burned and two youths were fatally shot Saturday.

An FBI spokesman said no arrest warrants had been issued and declined to say whether the agents would return to the reservation area. An attorney for the U.S. Interior Department and two FBI agents met tonight with a local Bureau of Indian Affairs official and two leaders of a dissident faction within the Chippewa Indian tribe.About 3,000 Chippewas live on the reservation.

About 100 teen-agers rummaged through the burned-out ruins of the center and its garage, a post office, two grocery stores and two homes. About 45 burned-out pickup trucks and other vehicles littered the streets of the northern Minnesota town, and many other vehicles had windows shot out. The town of Red Lake, however, was relatively quiet.

The boys, aged 12 and 15, both died of gunshot wounds, but the FBI said the deaths could not immediately be linked to the Indians' dispute. However, Roger Jourdain, president of the Red Lake Tribal Council, said the death of the 15-year-old, Vernon Lussier, was connected with the siege. The second youth was identified as Alan Cloud.

Jourdain and Celestine Maus, BIA superintendent on the reservation, were taken to the jail in nearby Bemidji early today for their own protection, according to a source who decliend to be identified.

After two meetings tonight between federal officials and dissident leaders, Interior Department headquarters in Washington agreed to replace Maus as superintendent, acording to Tom Crawford, editor of the Bemidji Pioneer, who attended the second meeting. He ascribed the agreement to Forrest Garard, assistant secretary for Indian affairs.

The violence erupted early Saturday when a group of 50 to 75 Indians took over the Red Lake Law Enforcement Center and locked four police officers in the jail, authorities said. The officers were release unharmed but shooting broke out later.

Witnesses said police cars and other vehicles were set on fire and that flames spread to the center garage and the main building, heavily damaging both.

The violence apparently resulted from a dispute over the ouster of the council reasurer, Stephanie Hanson, who had questioned council finances. Hanson's husband, Harry, was believed to be a leader of the dissidents and the FBI and a local newsman were attempting to negotiate with him today.

Hanson reportedly said he would surrender only under certain conditions, among them reinstatement of his wife as council treasurer and an investigation of tribal affairs by the FBI and Minnesota's U.S. senators.