Several thousand Iranians marched through the streets of Tehran today in the first such protest against the excesses of Ayatollah Ruhollah Khomeini's revolutionary committees.

The protesters, mostly university and high school students, were angered by one committee's arrest Thursday morning of two sons and a daughter-in-law of a respected and relatively liberal religious leader.

The three, known for their leftist leanings, were taken to a military barracks where they were held for 16 hours before being released.

The religious leader, Ayatollah Mahmoud Taleghani, 72, who has been a close associate of Khomeini, subsequently closed his Tehran office to protest the arrests and left the city for an undisclosed distination.

According to seasoned observers here, what might be dubbed "the Case of the Missing Ayatollah" underscores the increasing strains in Khomeini's revolutionary organizations and indicates the possibility of a rift in the Moslem religious leadership.

The incident also showed that many Iranians, notably members and sympathizers of guerrilla groups on the left and right, are getting fed up with the highhandedness of the committees of Khomeini followers that have enjoyed the power to make arbitrary arrests and searches. Unstated is the concern of these other groups that they, and not only Iranians associated with the deposed Shah, could eventually become the targets of a crackdown.

Tehran newspapers quoted a statement from Ayatollah Taleghani's office saying he was going underground for a while to protest "the trampling of the rights of the Iranian people." The statement blamed "irresponsible elements" who maintain "illegal jails," and said the incident "made the avatollah physically and spiritually unwell."

Taleghani, who was tortured during more than 10 years of imprisonment by the shah's secret police, SAVAK, has built up a personal following in Iran, especially among students, because of his relatively liberal attitudes on a number of issues. He has good relations with guerrilla groups, including the Marxist Fedaye, and has played a key trouble-shooting role on behalf of the new government in trying to quell agitation by independent-minded Kurds and Turkomans in northwestern and northeast Iran.

The motive for the arrests of Taleghani's sons and daughter-in-law was unclear, but many Iranians suspected they were linked with reports of his protests to Khomeini about the arrogant behavior of the revolutionary committees acting in his name. The dispute apparently has been over the committee's acting as a law unto themselves, rather than the current wave of summary trials and executions of former shah supporters.

Deputy Prime Minister Abbas Amir Entezam said the government had no prior knowledge of the arrests and was sorry they occurred. He said those responsible, identified by newspapers as militiamen of a revolutionery committee based in north Tehran, had been acting on their own.

"The implication, though, is that this could lead to rift between Taleghani Khomeini because the committees are acting in Khomeini's name," one veteran observer said.

The regime's "revolutionary prosecutors" today banned further arrests and house searches by the committees in evident reaction to the public furor over the Taleghani incident.

Meanwhile newspapers reported the executions of nine more officials of the shah's government overnight, one in Tehran and eight in the provinces. More than 7o persons have been shot by revolutionary firing squads since trials resumed 10 days ago, and more than 120 have died since February.