Israel's attorney general has accepted a recommendation by a special investigating commission that an Army general implicated in beating to death two Palestinian hijackers in a bus in the Gaza Strip last April not be charged with homicide.

However, Attorney General Yitzhak Zamir recommended that paratroop Brig. Gen. Yitzhak Mordecai be court-martialed on charges of causing grievous bodily harm and conduct unbefitting an officer.

Although the commission report released tonight cited evidence that Mordecai pistol-whipped the two prisoners after they were taken off the hijacked bus for interrogation, Zamir said it was impossible to determine if the prisoners died as a result of those blows or from injuries sustained in the original assault on the bus.

One woman soldier was killed when four Palestinian hijackers commandeered the bus in Ashkelon on April 12, 1984, and drove it to the Gaza Strip, where security forces disabled the vehicle and killed two of the terrorists while storming it in a hail of gunfire. Two other hijackers were photographed being led away from the bus, apparently without serious injury, but they died later in a hospital.

Investigators found that the prisoners were beaten while Mordecai was attempting to determine whether a bomb was still on the bus.

The commission recommended, and Zamir concurred, that five members of the Shin Bet secret internal security force and three policemen be charged with using unnecessary force and conduct unbecoming to their office.

The attorney general's recommendation of court-martial for Mordecai is not binding, but military sources said that some disciplinary action against the general is likely.