Undeterred by the arrest of hard-line protest leaders, thousands of Muslims marched in Indonesia’s capital on Friday, calling for the jailing of the city’s minority Christian governor.

Following Friday prayers, the protesters marched from Istiqlal Mosque in central Jakarta to the nearby presidential palace, which was under heavy police guard.

Protests against Gov. Basuki “Ahok” Tjahaja Purnama have snowballed since September when he was accused of blaspheming the Quran and subsequently charged. His trial is still underway.

The turnout for Friday’s protest was small compared with the hundreds of thousands who answered the call of hard-line Islamic groups to flood central Jakarta for demonstrations in November, December and February. Jakarta police’s director of traffic Ermayudi Sumarsono estimated the crowd at 13,000 to 15,000. Police estimates are often conservative.

Earlier on Friday, police said they had arrested Muhammad Al Khaththath, the leader of the Muslim Peoples Forum umbrella group, and several other activists for suspected treason.

“We are not cowed by the arrest of our leaders,” said a protester who identified himself as Wahyudi. “We’ll keep fighting for the dignity of Islam. There’s no room for kafir to lead in this nation.”

The blasphemy case, slurs against Mr. Ahok’s Chinese ethnicity and the ease with which hard-liners attracted huge numbers of people to protest have undermined Indonesia’s reputation for practicing a moderate form of Islam and shaken the secular government as well as mainstream Muslim groups.

Blasphemy is a criminal offense in Indonesia, punishable by up to five years in prison.

Mr. Ahok will compete in a runoff election for governor next week against a former cabinet minister backed by conservative Muslim clerics.

Opponents seized their moment last year when a video surfaced of Mr. Ahok telling voters they were being deceived if they believed a specific verse in the Quran prohibited Muslims from electing a non-Muslim as leader.

Jakarta police spokesman Argo Yuwono said Al Khaththath and the other activists were arrested early Friday. Local media said one of those men was the deputy coordinator for Friday’s protest.

It was the second round of arrests for suspected treason related to anti-Ahok protests. Police rounded up 10 people including high-profile citizens after a Dec. 2 protest turned violent, with dozens injured and one person killed by tear gas side-effects. They were all subsequently released.

Wiranto, the top security minister, met with representatives of the protesters and said he reiterated that the government won’t interfere in Ahok’s trial.

Effendi Lubis, who traveled from Bogor in West Java for the demonstration, said Muslims would continue protesting until Mr. Ahok is in prison.