CLARKSBURG, W.Va. (AP) _ A federal jury found the leader of the nation's largest Hare Krishna community innocent of arson and fraud charges today, but convicted a follower of burning an apartment building to collect $40,000 in insurance.

The U.S. District Court jury deliberated about three hours over two days before clearing Kirtanananda Swami Bhaktipada of conspiracy, arson and mail fraud charges.

Jurors, however, found Thomas Drescher, 39, also known as Tirtha Swami, guilty of charges of malicious burning in the fire in the vacant two-story building near the Krishnas' New Vrindaban community in Marshall County.

U.S. Attorney William Kolibash said his wide-ranging investigation of the community will continue.

''You heard the verdict,'' Kolibash said as he left the courtroom. ''The jurors did their job. We did ours.''

Bhaktipada, 50, who spent much of the morning reading a Bible, said the case should have never been tried and that it was part of a harassment campaign.

''That they would go to so much trouble for $40,000 fraud doesn't make any sense at all,'' he said, smiling. ''If that's not religious persecution, I don't know what is. Don't forget, Marshall County is the same county that ran the Mormons out a hundred years ago. Bigotry runs deep in these woods.''

Drescher's attorney said he would appeal his client's conviction on charges of malicious burning. The charge carries a possible 10-year prison term and a $10,000 fine. Drescher was cleared of conspiracy and mail fraud charges.

The case went to the jury after James Lees, attorney for Bhaktipada, argued that key government witnesses tailored their testimony to please federal prosecutors.

''It was the bad guy who created the investigation,'' Lees said Monday. ''This isn't the United States government going after the bad guy. This is the other way around.''

The arson and conspiracy counts carried maximum penalties of 30 years and $750,000 in fines. The mail fraud charges are punishable by up to 25 years and $1.25 million in fines, said Kolibash.

Lees and Mark Karl, representing Drescher, on Monday attacked the integrity of prosecution witnesses Howard Fawley, the former treasurer of the Krishna community at New Vrindaban, and Daniel Reid, his former assistant.

Fawley has pleaded guilty to one count of mail fraud stemming from the case. Reid pleaded guilty to one count of voluntary manslaughter in the slaying of Charles St. Denis, a fringe member of New Vrindaban who lived at the burned building.

Fawley testified that Bhaktipada asked about the fire insurance on the building before it was burned.

Reid, who is serving a sentence of one to five years, said Bhaktipada said ''yes'' and nodded when he asked if he wanted the structure burned on July 14, 1983.

Bhaktipada, who testified last week, disputed testimony by his former treasurer that he approved a plot to burn the apartment building in a scheme to collect the insurance money.

Bhaktipada has maintained the charges are part of a $4 million effort by the federal government to harass the community, located about 70 miles southwest of Pittsburgh.

Drescher, who was convicted of first-degree murder in the June 1983 killing of St. Denis, did not testify during the trial. Drescher is serving a life term without the possibility of parole at the West Virginia Penitentiary.

He is also fighting his extradition to California to face a murder charge there in the death of Krishna dissident Steve Bryant of Detroit. Bryant, a former resident of New Vrindaban, was shot to death in May 1986 as he sat in his van on a Los Angeles street.