An Israeli soldier and two Moslem militiamen were killed in southern Lebanon today during a clash between units of the Israeli and Lebanese armies near the line that separates the forces, the Israeli military command announced here.

The battle, which reportedly lasted about two hours and in which both sides were said to have used tanks, was the most serious incident to date between the two armies. It occurred two weeks after a similar Israeli-Lebanese clash in virtually the same spot, near the village of Kawthariyet Siyad.

The Israeli soldier who was killed was the fourth to die in southern Lebanon since Israel began its three-stage withdrawal from the territory last month.

Each country blamed the other for initiating the fighting. A military communique issued in Beirut said an Israeli force, including tanks and helicopters, advanced on a Lebanese Army position behind a screen of fire. Reports from Beirut said two militiamen from the Lebanese Moslem Shiite militia Amal, who had joined the fighting, were killed, and that several Lebanese Army soldiers were wounded in the exchange of fire.

An Israeli Army statement said one of its patrols encountered several suspected guerrillas and pursued them toward Kawthariyet Siyad when they refused to halt. Lebanese Army soldiers stationed in the village, which is beyond the current Israeli zone of control in southern Lebanon, opened fire on the pursuing patrol, and the Israeli soldiers returned the fire, according to the announcement.

The Israelis provided no further details. Israeli radio said tonight that military officials here considered the incident "very serious" but believed it was the result of a "misunderstanding."

In a similar incident on Feb. 27, the Israelis said Lebanese Army soldiers opened fire at one of their patrols while it was pursuing two armed men. The Israelis responded with a single cannon shot from a tank and the earlier incident ended without casualties on either side. In both cases, the men the Israelis said they were pursuing escaped.

The area where the two Israeli-Lebanese clashes have occurred is about six miles northwest of the southern Lebanese city of Nabatiyeh, just north of the line that separates the Israeli-occupied zone and the territory that Israel evacuated last month. The Israeli Army has not established fixed positions on this new, temporary line, but patrols it frequently with armored vehicles and soldiers.

Meanwhile, the Israelis today continued their searches of Moslem Shiite villages east of the port city of Tyre, an area that has been the center of Lebanese resistance to the Israeli occupation. Timor Goksel, the spokesman for the United Nations peace-keeping force that is stationed in southern Lebanon, said Israeli forces searched two villages today. In the first, Hallusiyat, Goksel said the Israelis destroyed four houses and arrested eight men. He said that in the second village, Tair Filsay, 14 men were arrested but there were no reports of houses being destroyed.

Goksel also said that three Lebanese women in the village of Yatar were wounded yesterday during a shooting incident between militiamen of the Israeli-backed South Lebanon Army and gunmen who fired at them as they attempted to enter the village.

Goksel said that the body of a 16-year-old girl, apparently shot in the head during the incident, was later found in the village. He said the Lebanese militiamen, who were accompanied by civilian Israeli security agents, retreated from the village, leaving behind three automobiles that were burned by local residents.

The U.N. spokesman also said that early today the South Lebanon Army militiamen attempted to block entrance to the village by an Irish unit from the U.N. force.

Israeli military officials confirmed that there had been a shooting incident at Yatar, but said only one woman and one South Lebanon Army militiaman were wounded. The officials denied that the militiamen attempted to interfere with the Irish unit of the U.N. force