"Working with the Ethiopian government, we were able to process their repatriation and they are all safely in Uganda," Uganda's internal affairs ministry spokesman, Simon Mundeyi, told AFP.
The followers of Church Christ Disciples from Soroti travelled to Ethiopia in February after their pastor claimed they would find Jesus there after 40 days of fasting, Mundeyi said.
"A joint security and intelligence team has put the religious cult leader, Pastor Simon Opolot, who is a Ugandan, on the wanted list and he will be apprehended."
He said the followers were drawn from across Soroti, a largely rural area, and told to sell all their possessions because the world was coming to an end.
"They were fasting for 40 days and on the 41st day is when they were to meet Jesus Christ," said Mundeyi.
"But Ethiopian officials learnt of their arrival in the country, picked them (up) and confined them until their repatriation documents were ready."
Authorities in Uganda were alerted to the plan by concerned residents in Soroti after the cult followers began leaving for Ethiopia.
In 2000, some 700 members from the Movement for the Restoration of the Ten Commandments of God in Uganda burned to death in one of the world's worst cult-related massacres.
Members of the cult, which believed the world would come to an end at the turn of the millennium, had been locked inside a church, with the doors and windows nailed shut from the outside.
The building in southwestern Uganda's Kanungu district was then set alight.
In neighboring Kenya, more than 250 people linked to a doomsday cult that also believed in extreme fasting have been exhumed from a forest near the country's coast since April.
Cult leader Paul Nthenge Mackenzie is facing various charges in the grisly case, accused of driving his followers to death by preaching that starvation was the only path to God.
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