Indonesian President Joko Widodo has chosen a conservative Muslim cleric who has railed against homosexuality and once issued a fatwa against secularism as his running mate for next year's election.

Key points: Ma'ruf Amin is Chairman of the Indonesian Ulema Council

Ma'ruf Amin is Chairman of the Indonesian Ulema Council He was behind a religious order declaring liberalism, pluralism and secularism as against Islam

He was behind a religious order declaring liberalism, pluralism and secularism as against Islam Prabowo Subianto will run against Mr Jokowi in next year's election

Razor wire, along with dozens of police and secret service officers, held back jubilant crowds, as President "Jokowi" officially registered as a candidate for re-election.

"Democracy is not war, democracy is not hostility, but is a contest of ideas, track record and achievements," Jokowi said.

His pick for Vice-President, Ma'ruf Amin, is chairman of the Indonesian Ulema Council, the nation's top Muslim clerical body.

In 2005, Mr Amin was the key figure behind a fatwa, or religious order, that declared liberalism, pluralism and secularism as against the rule of Islam.

Many have expressed surprise that Mr Amin was selected while Justice Mahfud was overlooked, reportedly at the last minute. ( AP: Achmad Ibrahim )

"That had a really major impact on progressive Muslims who were trying to bring about a more tolerant and pluralistic form of Islam," said Associate Professor Greg Fealey from the Australian National University.

Associate Professor Fealey said Mr Amin would provide a "political shield" to Jokowi, who is sometimes accused of not being religious enough.

"Wherever there have been socially conservative campaigns run within the Islamic community in Indonesia, Ma'ruf Amin has often been right at the centre of those campaigns," he said.

The most prominent of those campaigns was mass protests against Jakarta's popular governor Basuki "Ahok" Purnama in 2016, over questionable accusations he committed blasphemy, which is illegal in Indonesia.

"[Amin] issued an opinion to say that that Ahok had been guilty of blasphemy and the government should take action against him," Associate Professor Fealey said.

"The moment that opinion was released, that really saw huge mobilisation within the conservative Islamic community against the governor."

Muslim protesters march during a protest against Jakarta's Christian Governor Basuki "Ahok". ( AP: Achmad Ibrahim )

Next year's election will be a re-run of the 2014 presidential poll, with former military strongman Prabowo Subianto declaring his candidacy once again.

Mr Prabowo, who was discharged from the military over allegations of torture by his men, has chosen Jakarta's wealthy Deputy Governor Sandiaga Uno as his vice-presidential running mate.

"We will fight for all Indonesian people, whatever their religion, whatever the tribe, whatever the ethnicity, whatever the race," Mr Prabowo said after officially registering his ticket.

This is Prabowo's fourth run at the presidency and is widely expected to be his last chance.