Swiss law enforcement sources, who asked not to be identified, declined to say whether a charge was specified in the arrest warrants for Luc Jouret and Joe di Membro, whose name also has been given by authorities as Joseph di Mambro.
It is possible in Switzerland to arrest someone for questioning as a witness to a crime, but the warrants were the first indication from authorities that they believe the two leaders are still alive.
Jouret and di Mambro visited their chalet hours before elaborately rigged bombs set off fires in it and other buildings associated with the cult, an investigator also said Friday.
Jouret, a Belgian doctor and the leader of the mysterious Order of the Solar Temple, and di Mambro had a locksmith let them into the chalet about 4 p.m. Tuesday, the investigating judge Jean-Pascal Jaquemet told Swiss radio.
The chalet was one of three that started burning about 3:30 the following morning, hours after fire destroyed a farmhouse and barn elsewhere in Switzerland.
Investigators are weighing new evidence, such as bullet wounds and weapons, suggesting at least some of the cult members found dead this week were murdered, and not willing participants in a mass suicide.
"We have elements now that clearly indicated there may have been an execution,'' said investigating judge Andre Piller.
Piller said that 20 of the victims had bullet wounds in their heads and evidence indicates they could not have shot themselves.
"There was certainly another person who put several bullets into the heads of these victims,'' he said.
However, Piller said the bullets could have been a "coup de grace'' intended to finish off victims who were still alive. No weapons were found near the bodies to indicate they had shot themselves.
Piller said he was considering whether the deaths involved both suicide of some and murder of others.
Canadian authorities said they were sure that a baby and two adults found in a burned house north of Montreal were murdered.
The latest finds brought to five the number killed in Canada. The Swiss toll is 48.
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