Deputy interior minister Anatoly Dzivitsky was quoted as saying that the 60 people occupying the building had left quietly and without resistance once the police intervened.
The group had threatened to commit mass suicide if forced to leave and several ambulances were on standby when police stormed the building.
The men were detained, while the women and 20 children were taken to a hospital near to the occupied administrative building in Yakutia, eastern Siberia.
The fundamentalist Christians had invaded the building Monday to protest against a January decision by residents of their village, Kutana, to expel them.
Their exact motives and goals for the occupation were unclear.
One member of the group Vitaly Kozyr, told the press after the Pentecostalists' evacuation that the group "forgives" the president and the government.
The group's leader "Pastor Yevgeny", has spent 13 years in jail for killing his wife, according to Russian news agencies.
According to the Russian daily Segodnia, the movement was born in the United States and registered in Russia in 1994.
It now boasts 46 branches in Russia, 1,155 churches and 900 Sunday schools.
The Russian authorities are becoming concerned at the spread of proselytising religions, including many recent imports from abroad.
A 1997 law on religious association limits their activities more than the traditional religions in Russia (Orthodox, Islam, Judaism, Buddhism).