For almost five years Indonesia did not execute a prisoner on death row. But since a Malawian drug smuggler broke that drought on March 15, the floodgates have opened. In the early hours of Friday, three people - all Indonesians and all murderers - were removed from their cells and shot.

The news will cause further dismay to Australian drug smugglers Myuran Sukumaran and Andrew Chan, who are on death row in Kerobokan prison. They lodged applications for clemency nine months ago with President Susilo Bambang Yudhoyono.

Friday's executions took place about 12.30am in the grounds of Nusakambangan island prison in Cilacap, Central Java, reporters said.

The prosecutor's office did not immediately confirm them, but ambulances were seen leaving the prison about 2am.

Those put to death were Suryadi Swabuana, Jurit bin Abdullah and Ibrahim bin Ujang. Suryadi was convicted of the premeditated murder of a family in Sumatra in 1991; Jurit and Ibrahim of a joint murder in Sekayu, South Sumatra, in 2003.

There are about 130 prisoners on death row in Indonesia, most for drug trafficking. Among the drug smugglers are 62 foreigners.

In March, after Malawian drug trafficker Adami Wilson was executed, the Attorney-General announced plans to execute at least nine people this year.

The Australian prisoners are unlikely to be among them as long as their clemency pleas remain undecided.

Human rights activist Al Araf said the executions ''cannot be separated from the 2014 elections''.

''The death penalty in Indonesia has a strong flavour of building political popularity,'' Mr Araf, from the human rights group Imparsial, said.

Amnesty International said the executions were ''a major setback … in a country that appeared to be moving away from the brutal practice''.

Spokesman Michael Hayworth called on the Australian government to ''immediately and unabashedly condemn the execution''.

''Just last week the Australian government restated its opposition to the death penalty. It is now time for the government to use its leadership role in the region to curb the practice of state-sanctioned killing,'' he said.