Prime Minister Menachem Begin, in a report to parliament on the weekend Palestinian terrorist attack that killed 45 persons, sternly warned yesterday that Israel would defend its citizens and "cut off the arm of the evil."

Begin's statement was seen here as further indication that Israel intends a retaliatory strike against the Lebanon-based Al Fatah organization, which has claimed responsibility for the attack, the bloodiest in Israel's history.

Palestinian commandos were on full alert at camps throughout Lebabon, according to reports from Beirut, and reinforcements were being moved into strategic areas such as Tyre, a Palestinian-controlled seaport in southern Lebanon.

Thunderstorms and heavy rains in the Israeli-Labanese border are yesterday made conditions unlikely for any immediately large-scale air or ground military activities, reports from southern Lebanon said.

Begin's report to the emergency session of parliament matched the angry and vengeful mood of the nation.

"Those who spill innocent blood will not enjoy immunity," he said. "We shall defend our citizens, our women and children. We shall cut off the arm of evil and we shall not allow under any conditions an evil hand to be lifted against the head of a Jewish child or woman."

Former Foreign Minister Yigal Allon, of the oppostion Labor Party, said, "We cannot let this incident pass unnoticed. I call on Isreal to use active defense in order to break the strength of the PLO" - the Palestine Liberation Organization, of which Fatah is a part.

Begin sharply criticized the Soviet Union for its support of the PLO and he called on nations where the PLO has opened offices to expel all PLO representatives.

The Israeli press was nearly unanimous in voicing its wrath. Even the dovish Al Hamishmar said that the PLO "must not be let off lightly. The hand of Israel will reach them wherever they may be and they will be punished."

If Israeli public opinion were to be the deciding factor, it would not be a question of whether there will be a punitive raid against the PLO but only when, where and how.

Begin also told parliament that civilian and military committees would be set up to investigate the attack and the performance of the Israeli security forces.

The attack began when two rubber rafts carrying 11 Palestinian commandos landed on a secluded beach about 40 miles north of Tel Aviv. The commandos seized a bus carrying Israeli tourists and forced the occupants of a second bus to join them as they rode toward Tel Aviv, firing at motorists.

At the northern edge of Tel Aviv, a police roadblock stopped the bus and, in an exchange of gunfire and explosions, the bus and many of its occupants burned. The death toll of the entire attack now stands at 36 Israelis and nine Palestinians. Two Palestinians were captured. At least 76 persons were wounded.

A great many questions are being asked about the coordination between various branches of the security forces.

Although it is generally recognized that it is impossible to completely seal off the entire Israeli coast, there is concern about the fact that the raiders managed to land undetected in broad daylight and to enjoy a meal on the beach, with wine, before they moved inland to ambush first a taxi and then two buses on Israel's busiest highway.

There is also criticism of the security forces for not blocking off the main highway as soon as it became known that the terrorists had a bus and were holding hostages. Many passing motorists were killed and wounded by random gunfire, as the raiders drove south with their hostages.

The manner in which the final ambush of the bus was handled, which resulted in the death of 25 people on the bus, is also being criticized.

Police sources said yesterday that the raiders - originally 13 in all - had been alunched from a larger ship into their rubber boots and two drowned before the rubber boat reached the beach.

The Palestinians apparently intended to land closer to Tel Aviv or on the beaches of the city itself as another group did in 1975. But they were forced to land to the north either because of heavy seas or because of police boat activity in the Tel Aviv area. Saturday was a particularly rough day at sea and there were many police boats off Tel Aviv assisting pleasure boats and sailors who were in trouble.

The Israeli Cabinet also met in special session yesterday to discuss the raid but no significant details of the meeting were given out.