Hundreds of armed Moslem Shiite demonstrators stormed the city hall of Baalbek in Lebanon's eastern Bekaa Valley this morning and virtually took over the entire town for the day.

Radio reports and eyewitness accounts said 500 members of the Lebanese Shiite organization known as Amal occupied the city hall building at 6:30 a.m. and proceeded to take down Lebanese flags and other bunting put up for Monday's celebrations marking the 39th anniversary of Lebanon's independence from France.

The demonstrators armed with automatic rifles and rocket-propelled grenade launchers painted slogans denouncing Lebanese President Amin Gemayel and Israel and hailing Iran's revolutionary leader, Ayatollah Ruhollah Khomeini, the reports said.

No injuries were reported in the takeover in Baalbek, a city of about 25,000 people, mainly Shiite Moslems. Also in the city is a contingent of about 300 Revolutionary Guards from Iran's Shiite-dominated government, who came this summer to help the Palestinians fight the invading Israeli Army. There was no indication that the Iranians were involved in today's siege.

However, the Shiites belonging to Amal in Baalbek are staunch supporters of the Iranian revolution. Their leader is Hussein Mousavi, who heads a breakaway faction of the national Amal organization under Nabih Berri.

The takeover on the eve of independence-day celebrations appeared to be aimed at discrediting Gemayel's government, which already is having serious difficulties containing the escalating sectarian strife between Moslem Druze and Christians in the Chouf Mountains southeast of the capital.

That area was tense but calm today after a shoot-out Friday night that left five Christian militiamen dead and five others, including four armed Druze villagers, wounded. It was the worst outbreak of violence there in two weeks.

Israeli tanks, armored personnel carriers and troops have moved in force into the Chouf in an attempt to quell the mounting sectarian fighting. But incidents like the shoot-out at Aytat Friday continue to occur regularly.

Gemayel, a Christian, called in Beirut for Lebanese of all religions to "be vigilant toward the dangers of dissension . . . for the neutrality and future of our country." In his address to soldiers he appeared to be referring to Lebanon's general problems, rather than specifically to events in Baalbek.

The Shiite demonstrators reportedly left the city hall in the early afternoon but maintained their control of the central square, which has been renamed after Khomeini, and set up checkpoints throughout the town.

Six policemen guarding the building were easily overwhelmed but were allowed to keep their pistols and set free after the demonstrators left the city hall.

Residents said their intention was to keep control of the city through Monday to prevent any independence-day celebrations.

They identified the demonstrators as Amal members and said many of them were known Shiites from Baalbek. The demonstrators, some wearing masks, told reporters only that they were "the people."

Baalbek is a well-known tourist attraction because of its well-preserved Roman ruins and also the center of Lebanon's flourishing trade in hashish.

The town has been highly politicized by the presence of the 300 Iranians, who have put up posters and slogans promoting Khomeini and his Islamic revolution throughout the town, including some of veiled women to promote the Shiite social tenets.

A Palestinian refugee camp, some guerrillas and units of the Syrian Army are also in the town, although it is basically under Amal's control.

It was not immediately known why Amal was so vehemently opposed to the independence celebrations or the Gemayel government, which has been trying to establish good relations with Syria and resisted signing any peace treaty with Israel.

But Baalbek and the entire Bekaa Valley is largely cut off from the politics of the capital and lives in a world of its own dominated by the 40,000 troops of the Syrian Army and the several thousand Palestinian guerrillas still stationed there.