A blast has hit a mosque packed with Shiite Muslim worshippers in northern Afghanistan killing at least 46 and wounding dozens in the latest security challenge to the Taliban as they transition from insurgency to governance.

The explosion tore through the mosque in the city of Kunduz during noon prayers, the highlight of the Muslim religious week. It blew out windows, charred the ceiling and scattered debris and twisted metal across the floor.

Area resident Hussaindad Rezayee said he rushed to the mosque when he heard the explosion, just as prayers started. “I came to look for my relatives, the mosque was full,” he said.

There was no immediate claim of responsibility for what Kunduz police said may have been a suicide attack, but militants from a local affiliate of the so-called Islamic State group have a long history of attacking Afghanistan’s ethnic and religious minorities.

The worshippers were Hazaras, who have long suffered from double discrimination as an ethnic minority and as followers of Shiite Islam in a majority Sunni country.

IS has been behind a rise in attacks, including against the Taliban, since the departure of US and Nato forces from Afghanistan at the end of August.

IS and the Taliban, who seized control of the country with the exit of the foreign troops, are strategic rivals. IS militants have targeted Taliban positions and attempted to recruit members from their ranks.

In the past, the Taliban managed to contain the IS threat in tandem with US and Afghan air strikes. Without these, it remains unclear whether the Taliban can suppress what appears to be a growing IS footprint.

The militants, once confined to the east, have penetrated the capital of Kabul and other provinces with new attacks.

It comes at a critical moment as the Taliban attempt to consolidate power and transform their guerrilla fighters into a structured police and security force.

While the group attempts to project an air of authority through reports of raids and arrests of IS members, it remains unclear if it has the capability to protect soft targets, including religious institutions.

In Kunduz, police officials were still picking up the pieces on Friday at the Gozar-e-Sayed Abad Mosque

Citing preliminary reports, the deputy Taliban police chief of Kunduz province, Dost Mohammad Obaida, said more than 100 people had been killed or wounded, and that he believed the dead outnumbered the wounded.

An official at the Kunduz provincial hospital said at least 25 people had been killed and 51 wounded. He said the figures were preliminary because casualties were being transferred to private hospitals as well.

Even the preliminary death toll of 25 is already the highest in an attack since foreign troops left Afghanistan.

The United Nations mission in Afghanistan condemned the attack as “part of a disturbing pattern of violence” targeting religious institutions.

Mr Obaida pledged to protect minorities in the province. “I assure our Shiite brothers that the Taliban are prepared to ensure their safety,” he said.

A prominent Shiite cleric, Sayed Hussain Alimi Balkhi, condemned the attack and called on the Taliban to provide security for the Shiites of Afghanistan.

“We expect the security forces of the government to provide security for the mosques since they collected the weapons that were provided for the security of the worship places,” he said.

The new tone struck by the Taliban, at least in Kunduz, is in sharp contrast to the well-documented history of Taliban fighters committing a litany of atrocities against minorities, including Hazaras.

The Taliban, now feeling the weight of governing, employed similar tactics to those of IS during their 20-year insurgency, including suicide bombings and shooting ambushes, and they have not halted attacks on Hazaras.

Earlier this week, a report by Amnesty International found the Taliban unlawfully killed 13 Hazaras, including a 17-year-old girl, in Daykundi province, after members of the security forces of the former government surrendered.

In Kunduz province, Hazaras make up about 6% of the population of nearly a million people. The province also has a large ethnic Uzbek population that has been targeted for recruitment by IS, which is closely aligned with the militant Islamic Movement of Uzbekistan.