Indonesia President Joko Widodo today named two former ministers in his latest Cabinet reshuffle – prominent reformist Sri Mulyani Indrawati, and controversial ex-military chief, Wiranto.

Indrawati, currently a World Bank managing director, has been appointed as finance minister, a post she previously held from 2005 until 2010.

The appointment of Wiranto as the country's top security minister, however, has activists calling it a step backwards for human rights.

Wiranto is among senior officers indicted by United Nations prosecutors over gross human rights abuses during Indonesia's 24-year occupation of tiny East Timor.

Around 100,000 people are estimated to have been killed, mainly by Indonesian forces and their proxies, or died of starvation and illness during the occupation, which occurred during dictator Suharto's three-decade rule.

Wiranto, who like many Indonesians goes by one name, was head of the armed forces when the Indonesian army and paramilitaries went on a bloody rampage in East Timor after it voted to become independent in 1999.

He denies any wrongdoing has never faced court over the atrocities.

He replaces Luhut Panjaitan in the key role of chief security minister, overseeing five ministries including foreign, interior and defence. Observers suggest Panjaitan caused concern among the military elite and Islamic groups by taking unprecedented steps to probe a bloody 1960s purge of communists and their supporters.

"It is a setback," Andreas Harsono, Indonesia researcher for Human Rights Watch, told AFP.

"The message might be that Jokowi (President Joko Widodo) is not going to be as progressive as before in pursuing his human rights agenda."

Panjaitan moved to the post of coordinating minister for maritime affairs, still a key job at a time Indonesia is embroiled in rows with China over the South China Sea.

Despite the claims against him, Wiranto has managed to maintain a prominent position in Indonesian public life. In 2014 elections he was a presidential candidate, although did not make it to the run-off, and in 2009 he was the running mate of Jusuf Kalla, the current vice president.

East Timor formally became independent in 2002.

Widodo announced thirteen changes to his cabinet in the reshuffle, his second since taking power in 2014.