The campaign of Prabowo Subianto, a former general and head of the special forces Kopassus, has been dogged by accusations that his unit kidnapped and tortured students during the 1998 riots that accompanied the overthrow of Suharto, as well as concerns over his long military career including actions in East Timor, West Papua and Jakarta.

But Jusuf Kalla, the man announced on Monday as the running mate of cleanskin Joko Widodo, also had questions to answer, said Human Rights Watch Indonesia researcher Andreas Harsono.

“Jusuf Kalla's stance on religious freedom is worrying,” Mr Harsono said. “In October 1969, the 26-year-old Kallaallegedly led attacks against more than a dozen Christian churches and schools in Makassar. He was never questioned for his role.”

The comment relates to raids in October 1969, when the Muslims’ Student Association attacked Protestant and Catholic churches, a nuns' dormitory, a theological academy and Catholic schools. Mr Kalla was head of the organisation at the time.

According to Mr Harsono, in 2006, as vice-president to Susilo Bambang Yudhoyono, Mr Kalla also agreed to pass a government regulation which “makes it very difficult for minorities to set up houses of worship”.

He said Mr Kalla had “consistently blocked efforts to build [the Christian] GKI Yasmin church in Bogor despite a Supreme Court decision to have it built”.

The building was blocked by the local Muslim majority who objected to having a Christian church in its midst, even though it had fulfilled all legal requirements.

Mr Kalla was also recorded at a 2009 rally held by the thuggish paramilitary organisation Pemuda Pancasila (Pancasila Youth) praising gangsterism and encouraging violence.

“Gangsters are people who work outside of the system, not for the government,” he told the rally. “The word gangster [preman in Bahasa Indonesia] comes from ‘free men’. This nation needs ‘free men’ … We need gangsters to get things done; free, private men, who get things done. We need gangsters who are willing to take risks in business. Use your muscles! Muscles aren’t for beating up people. Although beating people up is sometimes needed.”

Mr Prabowo’s alleged human rights offences are better known. He was dismissed from the Indonesian military in 1998 for kidnapping student activists.

“Prabowo refused to answer a summon from Indonesia's National Commission on Human Rights, deciding to go into self-exile in Jordan,” Mr Harsono said. “Prabowo later claimed that he had kept the activists alive but 13 activists are still missing. Prabowo also has a questionable role in the 1983 massacre in Kraras, East Timor.”

Mr Prabowo, who is officially banned from visiting the United States over human rights concerns, has consistently defended his record, denying some allegations and saying of others that he was acting on orders.

Mr Harsono also drew attention to the platform of Mr Prabowo’s party, Gerindra, which talks about "purification" of religion and taking action against "heresy".