After more than eight years in jail, the five Bulgarian nurses and a Palestinian doctor who recently took Bulgarian citizenship were freed on Tuesday under a cooperation accord between Tripoli and the European Union.
Georgi Parvanov, the Bulgarian president, pardoned them upon their arrival in Sofia. The EU newcomer and its allies in Brussels and Washington say the medics are innocent and point to evidence the epidemic began before they started working in Libya in 1998.
Bulgaria's foreign ministry said it had received a formal protest note on Wednesday in which Libya said it had not complied with a 1984 extradition treaty.
"There is also an article that says once prisoners are transferred, they are treated under the host country's legislation. The pardon has been legally done. There are no legal problems"
Boris Velchev, Bulgaria's chief prosecutor
Sergei Stanishev, Bulgaria's prime minister, said his country did not breached the agreement.
"It is understandable that Libya is reacting under existing pressure from the families of the infected children ... Bulgaria's decision [to pardon the medics] is motivated and fair," state news agency BTA quoted Stanishev as saying.
A diplomatic source told Reuters news agency that Libya had intended the medics to serve their remaining sentences after their transfer and referred to an article in the prisoner exchange agreement to that effect.
Jailed since 1999, the six were twice condemned to death. Last week Libya commuted the sentences to life in prison after the 460 HIV victims' families were paid $1 million each in a settlement financed by an international fund.
Boris Velchev, Bulgaria's chief prosecutor said the pardon was legal.
"There is also an article that says once prisoners are transferred, they are treated under the host country's legislation. The pardon has been legally done. There are no legal problems," he said.
More than 50 of the children have died and emotions are still high in the city of Benghazi, where the outbreak occurred.
Relatives of the children have said the infections were part of a Western attempt to undermine Muslims and Libya.