The Yugoslavia war crimes tribunal in The Hague convicted Plavsic in February 2003, but agreed last month to grant her an early release.
Relatives of the Bosnian Muslim victims of the 1992-95 war have protested against her early release.
The Swedish prison and probation service said in a statement: "Plavsic was transported this morning to [Stockholm airport] Arlanda. There she was picked up by a plane. What happens hereafter is up to her."
Murat Tahirovic, head of an association of Muslim and Croat war camp prisoners, said: "It might be in line with international law, but it has nothing to do with justice.
"How can we explain this to children whose parents had been killed [in Serb-run camps], children who remember their parents only from photos?" he said.
Plavsic, 79, was one of three members of the presidency of the Serbian Republic, headed by Radovan Karadzic, who on Monday boycotted the start of his trial at The Hague on 11 counts of war crimes and crimes against humanity, including genocide at Srebrenica.
Reduced sentence
Plavsic pleaded guilty in 2003 to persecution on political, racial and religious grounds by "inviting paramilitaries from Serbia to assist Bosnian Serb forces in effecting ethnic separation by force".
But instead of the 15 to 25 years the prosecution had requested, Plavsic was sentenced to 11 years for crimes against humanity including persecution, deportation, unlawful detention and cruel and inhuman treatment.
Charges of genocide, extermination and murder were dropped as part of a plea bargain.
Known as the "Iron Lady" for her leadership, the former Karadzic ally publicly supported the campaign of persecution against non-Serbs during the war.
Plavsic once defended her purge of non-Serbs as "a natural phenomenon" and not a war crime.
The former biology professor surrendered voluntarily to the International Criminal Tribunal for ex-Yugoslavia (ICTY) in January 2001.
She gave an unprecedented "mea culpa" in 2002, changing her plea to guilty to one count of crimes against humanity in the war.
Plavsic is the highest-ranking official of the former Yugoslavia to have acknowledged responsibility for the atrocities committed in the Balkan wars in the 1990s.