BEIRUT, Lebanon (AP) _ Syria's military intelligence chief in Lebanon pledged Wednesday to protect the kidnap-plagued American University of Beirut and other educational institutions.

In a statement broadcast by state-run Beirut Radio, Brig. Gen. Ghazi Kenaan declared: ''Freedom of political activity at AUB and outside the university will be protected. But we will be very strict in dealing with any security threat or armed act.''

The university's 5,000 students staged a daylong strike Tuesday to protest a pre-dawn campus raid by Syrian commandos in which 15 students, representatives of feuding Moslem militias, were rounded up for questioning.

The peaceful protest on the west Beirut campus was the first against the 7,500-strong Syrian intervention force sent into the capital's Moslem sector Feb. 22 to quell factional fighting.

Several pistols and submachine guns were seized in the five-hour Syrian operation that police described as a warning to students to halt militia activities on campus.

Police said most of the students detained Tuesday were freed nine hours later. A student spokesman claimed at least three students were unaccounted for Wednesday.

The crackdown was the first Syrian move to clean up the campus, where armed students have long operated without hindrance.

The American University of Beirut was once the most prestigious university in the Middle East. In recent years, its foreign staff have been targeted for assassination and kidnapping by Moslem militiamen opposed to Western influence.

Kenaan, who coordinates the Syrian forces' operations, said his soldiers have taken ''a number of steps to guarantee AUB's security and the safety of its students and teachers.''

He did not elaborate, but said: ''Any faction that tries to harm educational institutions will be severely dealt with.''

Less than half a dozen female American educators remain at the university, which once had a foreign faculty and staff of about 200. Nine Americans have been assassinated or kidnapped at the campus or in nearby districts since 1974.

Two American members of the university staff are considered hostages. Islamic Jihad claims it is holding Thomas Sutherland, of Fort Collins, Colo., the acting dean of agriculture, who was kidnapped on June 9, 1985.

Joseph James Cicippio, of the Norristown, Pa., area, the university's acting comptroller, was abducted Sept. 12, 1986. There was no immediate claim of responsibility.

The Syrians, at the invitation of Lebanese Moslem leaders, moved into west Beirut to stamp out a week of fighting between Shiite and leftist militias that left 300 people dead and 1,300 wounded.

The Syrians also imposed a nighttime ban on motorcycles in predominantly Moslem west Beirut Wednesday. Police said the order was apparently aimed at preventing hit-and-run sabotage attacks.

The dusk-to-dawn ban went into effect five days after Syrian soldiers confiscated hundreds of motorcycles in west Beirut without warning. They were returned to their owners on Wednesday.

Motorcycles, especially small-cylinder scooters, have become popular in Lebanon in the past two years due to fuel shortages and chronic traffic jams.