Indonesian police arrested five people, including a Muslim leader, for suspected treason on Friday, signalling a clampdown on hardline Islamist groups that have agitated against Jakarta's Christian governor ahead of a mid-April election in the capital.

The arrests came just before thousands of Muslims gathered to demand the sacking of Governor Basuki "Ahok" Tjahaja Purnama, who is on trial for blasphemy over accusations he insulted the Islamic holy book, the Koran.

Friday's rally was the latest in a series that have tested religious and ethnic tolerance in Indonesia, a secular nation with the world's largest Muslim population.

Vice President Jusuf Kalla called on the protesters to respect the legal process and said they would not be allowed to dictate the agenda.

"No matter how much pressure there is, we will not follow it. The government is firm against this kind of pressure," Kalla said in an interview with Reuters, referring to the rallies.

"Wait for the court's final decision (on Purnama)," he said.

Purnama, who is running against a Muslim candidate in the April 19 election, is backed by President Joko Widodo's ruling party. The sudden rise of fringe, hardline Muslim groups during the election campaign has raised questions about whether they are being used as political pawns and destabilising Indonesia.

The race to lead Jakarta is widely seen as a proxy battle for the presidency, which will likely be contested by Widodo and retired general Prabowo Subianto, who is backing Purnama's rival for the governorship of the capital.

Police have moved to contain mass anti-Purnama protests led by hardline groups like the Islamic Defenders Front (FPI) by detaining organizers and blocking Islamist propaganda online.

The movement's most prominent leader, Habib Rizeiq, was in January named a suspect amid allegations that he insulted the secular state ideology. He faces up to four years in prison if found guilty.

On Friday, Jakarta police spokesman Argo Yuwono said that five people had been arrested, including Muhammad Al Khaththath, a leader of the Islamic People's Forum (FUI), another hardline group that organised Friday's rally.

"We are charging them with conspiring to commit treason," Yuwono told broadcaster TVOne.

"There were several findings, including a plan to occupy the Indonesian parliament."

Thousands of protesters, clad in white and carrying anti-Purnama signs, gathered at Jakarta's grand mosque as police and military personnel blocked off roads leading to the presidential palace.

An estimated 20,000 people from various groups were expected to attend, police said this week, far fewer than the numbers seen at previous rallies.

Purnama, Jakarta's first ethnic Chinese Christian governor, remains popular for his efforts to cut red tape and ease the city's chronic traffic congestion and flooding. However, he faces a tight race with rival Anies Baswedan, a former education minister.