The Israeli Army imposed a curfew this week on the largest Arab town in the Golan Heights, the first curfew since Israel effectively annexed the Syrian territory.

The Israeli Army chief of staff, Lt. Gen. Rafael Eitan, confirmed in an Army radio interview today that the curfew had been imposed on the town of Magdal Shams, on the slopes of Mt. Hermon. He said the curfew was lifted after security forces completed their operation there.

Eitan's acknowledgment came after Syrian Radio said Israeli troops had conducted house-to-house searches in the town.

"We had to implement some current security measures, and for this we needed for preventive purposes to impose a curfew," Eitan said, without detailing the purpose. Army command spokesmen refused to elaborate on Eitan's statement.

Eitan said that some houses in Magdal Shams were searched for security purposes. The community of 12,500 Druze, members of an Islamic breakaway sect with secret tenets, is sharply divided among those who support Israeli annexation and those who remain loyal to Syria.

From time to time since Israel occupied the Golan Heights in 1967, the pro-Syrian faction has been subjected to security crackdowns, but today's curfew was the first since the parliament imposed Israeli "law, administration and jurisdiction" in the territory Dec. 14.

Eitan also said an Army alert along the northern border was prompted not only by anticipation of possible Syrian reaction to the annexation, but by a buildup of Palestine Liberation Organization forces in southern Lebanon.

Eitan said the alert will remain in effect for an "indefinite period," adding that the buildup of Israeli forces in the north has had a deterrent effect on both Syria and the PLO. Israeli General Urges Anti-PLO Initiatives

TEL AVIV, Jan. 1 (UPI)--A top military official in the occupied West Bank charged today that Israel is not challenging the PLO in the political arena with the same fervor it uses against Palestinian guerrilla activity.

Maj. Gen. Danny Matt, 54, who is about to retire from the military after three years in the sensitive post of coordinator of activities in the occupied territories, also charged that the mayor of Nablus, Bassam Shaka, is the commander of the Palestine Liberation Organization in the region and that the military government has been weak in moving against him.

Matt, in an interview on the Army radio, charged Israel has not challenged the political PLO with the same force that it counters PLO guerrilla attacks. He said Bir Zeit University in Ramallah was the center of anti-Israeli incitement and violence in the territories.

Matt has previously clashed with Shaka, who was maimed in a 1979 terrorist attack. In 1979, parts of a private talk between Matt and Shaka were leaked out of context to the press, leading to an Israeli military order to deport the mayor.

Shaka was jailed and went on a hunger strike, and all the other Palestinian mayors in the West Bank and Gaza resigned. There was widespread world pressure against the expulsion, and the military government finally canceled it.

Six months later, almost simultaneous car bomb explosions maimed Shaka and Ramallah Mayor Karim Khalaf. Shaka lost both his legs in the attack, and Khalaf lost one leg. The perpetrators are at large.

In today's interview, Matt said, "Bassam Shaka is actually the commander of the occupied territories for the PLO . . . I recommended he be expelled and I still think his expulsion is important."

Israel's fight against the PLO was "a paradox," the general said. While Israel reacts to every guerrilla attack with "every possible means, we don't fight with the same fervor against the political PLO in the territories."

"This is not the first time Matt has talked about me," Shaka said by telephone in reaction to Matt's remarks. "What he says is true, but he hides the real facts."

"All of our people in the occupied territories are behind the PLO and believe it is our sole representative," he said. "When Matt speaks of me, what he doesn't say is that I am one of all."