RAJNEESHPURAM, Ore., Sept. 21— The desert commune here that recruited homeless people from around the country last year, in what some local residents said was an effort to stack the voting in local elections, is once again in turmoil. A key leader has departed, and a string of allegations against her is being investigated by six law-enforcement agencies.

Indicative of the tremors that have rocked the commune was an offer last night by its spiritual leader, Bhagwan Shree Rajneesh, to give all but one of his 90 Rolls-Royces to his 5,000 disciples as a gesture of appreciation.

It was not accepted, however. The cars belong to the Rajneesh Investment Trust, which specifies that they be used exclusively by Mr. Rajneesh. The trust president, Swami Dhyan John, jumped in to say that because the guru had sat in all the vehicles, ''they are sacred and we want them just where they are.''

The offer of the cars came just a week after Mr. Rajneesh's principal adviser, Ma Anand Sheela, fled the commune with as many as 20 other leaders. Investigators are looking into allegations by the guru that Miss Sheela was involved in such crimes as attempted murder, wiretapping, arson and fraud, but have said they will not discuss whatever evidence they have collected.

Some observers outside the commune were skeptical of the guru's charges, suggesting he may have been trying to draw attention to Miss Sheela in an effort to shift focus from his own visa troubles.

Mr. Rajneesh also says that Miss Sheela was responsible for most of the activities that profoundly angered surrounding communities, including bringing 3,800 homeless people here last year to pack ballot boxes.

'Tired of Talking to Walls'

''I'm not much interested in uneducated, illiterate street beggars,'' he said.

Mr. Rajneesh emerged last October from three and a half years of self-imposed exile at the commune, saying little about it except that he ''got tired of talking to walls.''

He is pressing the argument that Miss Sheela, who he says was his only source of information in that period, used her position to impose ''a fascist state'' on the four-year-old commune. He acknowledges, however, that the key to her actions was his silence.

The authorities have set up shop on the commune to investigate for ''an indefinite period of time,'' according to Lieut. Dean Renfrow of the Oregon state police.

Mr. Rajneesh had been scheduled to meet today with agents of the Federal Bureau of Investigation and other law-enforcement officials to give evidence to support his allegations, but the meeting was later canceled, ''because of logistics,'' Lieutenant Renfrow said.

Miss Sheela and her friends have not answered the guru's charges. Before leaving, she said, ''There is so much disunity in the community and I'm so tired of trying to hold it together,'' according to a report in The Rajneesh Times, the commune newspaper.

Advocacy of Free Love

Mr. Rajneesh has said he has information that Miss Sheela first went to Germany and then to London, where he believes she is now.

During the stop in Germany she is known to have given an interview to the newsmagazine Stern, scheduled to appear Wednesday.

The commune has been dogged by controversy since Mr. Rajneesh transported it here from India in 1981. His teaching that there is no God has particularly angered local residents, as does casual nudity and cheerful advocacy of free love.

Residents of the commune say Miss Sheela, 35 years old, had taken an increasingly aggressive posture in recent years. A hit song on local radio stations last year was ''Shut up, Sheela.''

Some observers outside the commune say that Miss Sheela's public profile was highly contentious and that this is reason to be skeptical of the charges against her. They contend that she is the perfect scapegoat to curb mounting pressures to oust Mr. Rajneesh from the United States for overstaying his visa and to convince area residents that commune members have changed their ways.

Mr. Rajneesh has been providing ever more detailed allegations against Miss Sheela recently, contending that she and ''her gang'' of about 20, including most of the commune hierarchy, tried to poison him and his doctor, dentist and housekeeper.

The physician, Swami Devaraj, has asserted that he was apparently given poison on three separate occasions, but that his medical knowledge saved him.

Accidental Murder Alleged

Mr. Rajneesh adds that the homeless people were given nonlethal poisons to keep them docile, but that one derelict was accidentally killed.

''They just threw his body out of Rancho Rajneesh,'' the guru said, referring to the 64,000-acre property surrounding the commune. He appeared to be referring to the body of a 28-year-old homeless man found late last year on the south side of Mount Hood. An autopsy revealed his blood contained a mood-altering drug prescribed by the commune pharmacy. However, Lieutenant Renfrow said tonight that the inquiry into the death would be reopened as part of the larger investigation.

Other schemes were directed at local officials, the guru said. Many were antagonized in 1982, when the commune bought up most of the nearby town of Antelope 35 miles, changing its name to Rajneesh. This week Mr. Rajneesh has charged the group with being involved in an arson fire in Wasco County offices last year and planning to crash an explosives-laden airplane into another county office building. He has also alleged that the group was involved last year in causing a salmonella outbreak in The Dalles, the nearest larger town, by poisoning the water supply.

Representative James Weaver, Democrat of Oregon, has asked the Federal Bureau of Investigation to investigate, saying there was ''overwhelming evidence'' of sabotage.

The events leading to Miss Sheela's departure began with the guru's resumption of speaking, but things accelerated early this month when, he said, she told him she wanted to build a home in Rajneesh for victims of acquired immune deficiency syndrome, or AIDS. He said he rejected the plan as unsafe. Measures to Prevent AIDS The commune's measures against AIDS were a prominent topic of conversation here today. They include requiring the use of condoms, washing with pure alcohol before sexual relations and wearing rubber gloves during relations. Lately, kissing has also been prohibited for commune members.

Miss Sheela's replacement, Ma Prem Hasya, said she hopes to change the atmosphere markedly. ''We are going through changes every monent,'' she said. ''Creativity is beginning to flourish again.''

Still, she is not yet ready to relax the 12-hour-a-day, seven-day-a-week work pace, for which disciples are paid $10 a week, plus room and board.

But things seem to be getting back to normal. Wearing the required colors, pale tangerine to deep purple, couples bounced in the disco late into last night, and today the guru, flanked by two machine gun-toting guards, shared his revelations with followers for two hours.

Later he took a spin in one of his Rolls-Royces, a security helicopter hovering overhead.

Photo of Bhagwan Shree Rajneesh (UPI); photo of Ma Prem Hasya, the new pricipal adviser to Mr. Rajneesh, with a member of the commune, Swami David (AP); map locating Rajneeshpuram (NYT/Sept.22,1985)