Suryadi Swabhuana, Jurit, and Ibrahim, all Indonesians, were put to death by firing squad in Nusakambangan prison, on an island off the coast of the main island of Java.
"We executed the three men early Friday," said Mahfud Mannan, the deputy attorney general for criminal cases. "They were convicted in two separate cases of premeditated murder."
Swabhuana, 46, was convicted of murder and theft in 1991, according to government records.
Jurit and Ibrahim, who both go by one name like many Indonesians, were convicted of murder in a second case. Further details were not available.
Amnesty International slammed the latest executions as a "major regressive step".
"The executions set Indonesia against global trends towards abolition of the death penalty," said Josef Benedict, an Indonesia campaigner at Amnesty.
"Amnesty International calls on Indonesia to make (these) executions the last."
Andreas Harsono, from Human Rights Watch, added that President Susilo Bambang Yudhoyono "should immediately act to stop executions and practise what he preaches -- that Indonesia is a democracy that respects rights".
A number of foreign nationals are jailed on the resort island of Bali, mainly on drugs offences, and several are on death row.
This includes British grandmother Lindsay Sandiford who was sentenced to death in January for cocaine smuggling and two men from the "Bali Nine" group of Australians convicted of attempting to smuggle heroin.
Executions in Indonesia are usually carried out by firing squad in the middle of the night in isolated locations.
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