Nearly 2 1/2 months after he fell in his bathroom and fractured his thigh, Prime Minister Menachem Begin still suffers intense pain and, for the most part, is running the government by telephone from his home while he recuperates.

Although his aides have sought to dispel rumors that the 68-year-old prime minister is not healing as his doctors expected and that he has occasional bouts of depression over his lingering disability, Begin has sharply curtailed his activities and is seeing far fewer people each day than his job normally requires, according to informed official sources.

Begin broke his thigh on Nov. 26 and when he underwent surgery that night to repair it, his physicians termed his condition "excellent" and said he would stay in the hospital two weeks, followed by a convalescence at home for two to three weeks. They said patients who undergo such surgery usually are back on their feet "in a short time."

But Begin remained in the hospital for nearly three weeks and since his release Dec. 14 has only infrequently gone to his office, usually for about two hours in the morning. Although he is no longer confined to a wheelchair, he still is unable to move about without a portable walker and he has to be lifted in and out of his car.

Uri Porat, Begin's press secretary, today denied that the prime minister's ability to govern had been impaired or his temperament strained by the pain of his injury.

"The prime minister is not completely recovered yet, that is true. He has some difficulty physically, particularly when he is sitting an hour or two in the same seat. But his condition is getting better one day to the next and he is lucky to be in such good shape physically," Porat said.

Porat added that he expected Begin to be walking with the aid of a cane within a month or two.

Yesterday, Begin failed to attend the regular Sunday Cabinet meeting, turning over the chair to Deputy Prime Minister Simcha Ehrlich. Porat explained that in the morning Begin had considerable pain and, because he knew he had two meetings scheduled for the afternoon at his home, he decided to forego the Cabinet meeting.

"He didn't want to waste his energy on a Cabinet meeting that wasn't so dramatic. But he was still very much in charge," Porat said, noting that Begin drafted the Israeli response to the U.N. General Assembly resolution adopted Friday that urged sanctions against Israel for its annexation of the Golan Heights. Previously, some Cabinet meetings had been held at Begin's home.

Government sources said that although Begin early in December formally turned his duties over to Ehrlich, naming him acting prime minister, he never relinquished any significant control.

"He was in the driver's seat from the first day after the accident," said one official, noting that within hours after his release from the hospital Begin pushed the Golan Heights annexation through his Cabinet and then went to the parliament in a wheelchair to supervise its adoption.

Some ministers and other officials who have dealt with Begin in recent weeks, however, have complained privately that his temperament has been affected by the pain and the slowness of his recovery and that he has, on occasion, made vindictive personal attacks on his aides.

Finance Minister Yoram Arridor, in particular, came under a scathing, sarcastic attack by Begin as a result of a growing controversy over the effect on this year's budget of $270 million for property compensation for displaced Sinai Peninsula settlers, sources said. Even Begin's longtime confidant, Yaacov Merridor, chief economic consultant, was subjected to bitter attacks because of the budget feud, and the two friends have not met for weeks, sources said.

Begin is said to have become depressed by his inability to maintain contact with the public and to have brooded over being forced to cancel appearances.

Last week, he planned to address an international tourism conference here but he was forced to send a recorded message instead. Begin is said to have told aides that he will be unable to travel abroad for a year.

Also, legislation sponsored by the ruling Likud coalition has been held back because of the prime minister's disability, resulting in a backlog.

Begin reportedly has shown no signs of a recurrence of previous illnesses, including two heart attacks and a blockage of a brain artery that temporarily impaired his eyesight.