Three Hanafi Muslims who allegedly held 11 persons hostage at Washington's Islamic Center for 38 hours earlier this month and threatened to behead them were ordered jailed yesterday in lieu of $50,000 bonds.

The action by Judge H. Carl Moultrie I of D.C. Superior Court means that 11 of the 12 Hanafis charged with armed kidnaping at the Islamic Center and two other locations in the city are now behind bars.

Only their leaders, Hamaas Abdul Khaalis, 54, remains free on personal bond pending grand injury action in the case.

The release of Khaalis without money bond was part of the arrangement city officials negotiated to gain the freedom of the hostages at the Islamic Center and of 113 others being held by Hanafis at the District Building and at B'nai B'rith headquarters at 17th Street and Rhode Island Avenue NW.

The takeovers at all three sites began March 9 and ended in the early hours of March 11.

Later of the 11th, Judge Moultrie ordered six Hanafis jailed in lieu of $50,000 bonds and two jailed in lieu of $75,000 bonds. Khaalis and three others were allowed to go free without having to post money bonds.

It was these three that Moultrie ordered jailed yesterday. He said he acted because he now had testimony that at least two hostages at the Islamic Center had been injured and because of testimony that the three would follow the orders of Khaalis.

"It is the court's opinion that because of the willingness on the part of the defendants to take orders, the court had concluded that they may flee the jurisdiction if told to do so, based on their past actions." Moultrie said.

Moultrie made no mention of a motion by federal prosecutors that the three held on $50,000 bonds. The motion, which was filed Friday, emphasized that the agreement to let Khaalis remain free was good only until the grand jury acts. It emphasized that no agreements had been made concerning what charges would be brought, how they would be disposed of, or what the sentences might be if the defendants are convicted.

One person was killed at the district Building. U.S. Attorney Earl J.Silbert indicated during court hearings March 11 that the government would seek murder charges against all the alleged participants in the incidents.

The three Moultrie jailed yesterday are brothers. They are Abdul Rahman, 37, also known as Clyde C.Young; Abdul Rahim, 26, also known as Philip Alvan Young, and Abdul Quawee, 22, also known as Samuel L.Young.

They and six other Hanafis appeared in court for preliminary hearings, the sole purpose of which was to determine whether the cases should be bound over for grand jury action. Two Hanafis had preliminary hearings Friday. Khaalis is scheduled for a hearing March 31.

Until yesterday there had been no testimony of any violence against hostages at the Islamic Center on Massachusetts Avenue NW. But Det. Robert L.Chany of the D.C. police homicide squad told the court that a secretary at the center had cut her leg while being dragged from one room to another at the center and that a caretaker there had been beaten on the head and body.