Thousands of conservative Muslims protested in the Indonesian capital on Friday about the burning of an Islamic flag, sparking criticism from the government's top security minister that the country was in mourning after a plane crash and back-to-back natural disasters.

Waving black flags bearing the Islamic declaration of faith, several thousand demonstrators, many wearing white Islamic robes, filled a major thoroughfare in Jakarta after Friday prayers. It was the biggest of scattered protests since last month after a flag linked to a banned Islamic group was burned by members of the country's largest mainstream religious organization.

Video of members of Nahdlatul Ulama's youth-wing militia burning the Hizbut Tahrir flag has led to allegations of blasphemy because it was emblazoned with the Islamic declaration of faith.

Hizbut Tahrir, which seeks a global caliphate, has been banned by the Indonesian government as a threat to national unity.

Shortly before meeting with protest leaders, Indonesia's top security minister, Wiranto, said police had been "neutral and professional" in their response to the flag burning incident.

Blasphemy against any of the officially recognized faiths in Muslim-majority Indonesia is a criminal offense though prosecutions overwhelmingly target religious minorities.

Wiranto, who uses a single name, emphasized that Indonesia is dealing with the aftermath of a plane crash earlier this week that killed 189 people and earthquakes and a tsunami that claimed thousands of lives.

"The government will not ban the protest," he said.

"But they must not force their will, make people afraid or disturb public order," he said. "Moreover, our nation is currently in mourning after a series of disasters and a plane crash. They should help create peace, even the international community gives a lot of sympathy, empathy and assistance."

Religious and ethnic tensions are likely to rise in Indonesia as April's presidential election nears. President Joko Widodo has chosen a conservative cleric as his running mate to head off criticism he's insufficiently Islamic.

A protest was also staged Friday in Garut, West Java province, where the flag was torched after hard-liners allegedly infiltrated an event organized by Nahdlatul Ulama's youth wing.

Indonesia's moderate reputation was undermined last year when Jakarta's minority Christian governor was imprisoned for blasphemy following street protests against him that drew hundreds of thousands.