Three Nigerians and an Indonesian man were executed by firing squad in the wee hours of Friday morning for drug-related offences at the Nusakambangan prison island.
The Nigerians executed were Seck Osmane, Humphrey Jefferson Ejike and Michael Titus Igweh.
The Indonesian was named as Freddy Budiman.
Ten other convicts expected to have been killed along with the four had a last-minute stay of execution.
Those awaiting executions include three Indonesians, a Pakistani, an Indian, one Zimbabwean and four other Nigerians.
Amnesty International condemned the killings as a “deplorable act” that violated local and international law.
Indonesia’s Deputy Attorney-General Noor Rachmad said it was “not a pleasant thing but it was to implement the law”.
“The executions are only aimed at halting drug crimes,” he said, adding that the rest “will be carried out in stages”.
Indonesia has some of the world’s toughest drug laws, and has faced intense criticism internationally for resuming executions.
In April 2015, the execution of 14 drug convicts, mostly foreigners, was widely criticised.
Australia briefly withdrew its ambassador from Indonesia in protest over the execution of its citizens, Andrew Chan and Myuran Sukumaran.
Indonesian President Joko Widodo vowed to take a hard line against drug trafficking when he was elected in 2014, saying he would not compromise over death sentences to convicted drug dealers.
This is the third round of executions under Widodo.