The group has claimed responsibility for both attacks, the most recent of which saw a group of bombers shoot their way into the largest Shia mosque in Kandahar province – the Taliban’s spiritual heartland – before blowing themselves up among the worshippers.
At least 47 people have died and fatalities among the 70 wounded are expected to rise – just a week after 80 worshippers were thought to have been killed in a similar attack during Friday prayers at a packed mosque in Kunduz.
Under the Sunni Taliban’s new rule, Shia mosques have so far been guarded by local volunteer forces with special permission to carry weapons.
But Kandahar’s police chief has now said that units will be assigned to protect them.
“Unfortunately they could not protect this area and in future we will assign special security guards for the protection of mosques and Madrasas,” he said in a statement posted on Twitter by a Taliban spokesman.
Attacks on Shia mosques and targets associated with the Hazara ethnic minority, who make up the biggest Shia group in Afghanistan, were regular occurrences under the toppled Western-backed government.
There has been deep shock as the attacks have continued since the Taliban seized power in August, tarnishing the Islamists’ claim to have brought peace to Afghanistan after decades of war.
Since the takeover, Isis-K has conducted dozens of operations – from small scale attacks on Taliban targets to large-scale operations such as Friday’s bombing at the Fatima mosque.
The official toll from the attack in the southern city of Kandahar stood at 47 dead and 70 wounded but the toll could still rise further. On Saturday, large crowds gathered to bury the white-shrouded victims in a mass grave. In total, 63 graves were dug.
“There are so many who have lost body parts, and among those in hospital in serious condition, I don't know how many more numbers will be added to the death toll,” said community elder Hajji Farhad.
The death toll in Kunduz was unknown, but health officials initially suggested 70 to 80 lives were lost, while other reports suggested more than 100 people were killed.
Shia leader Sayed Mohammed Agha called on the Taliban government to take serious measures to protect the religious minority, “because our enemies will harm our society by any means they can”.
The United Nations has condemned both attacks, which it warned was “part of a disturbing pattern of violence” which “highlights the vulnerability of ordinary Afghans, especially religious minorities”.
On Friday, UN secretary general Antonio Guterres said he condemned the “despicable” attack “in the strongest terms”, adding: “The perpetrators of this latest crime against civilians exercising their right to freely practice their religion must be brought to justice.”
Isis first announced its expansion to the Khorasan region in 2015, which historically encompassed parts of what is now Iran, Central Asia, Afghanistan, and Pakistan, according to the Centre for Strategic and International Studies (CSIS).
Within three years of its emergence, the terror group had carried out more than 100 attacks on civilians in Afghanistan and Pakistan, and had been involved in some 250 clashes with the US, Afghan, and Pakistani security forces, CSIS said, citing the Armed Conflict Location & Event Data project.
The Pentagon has admitted that “thousands” of Isis-K members prisoners were released by the Taliban after it took over the United States’ Bagram air base as it seized the country in August.
Describing the recent mosque attacks as a move to “go directly into the Taliban heartland in Kandahar and go after civilian populations there specifically”, and something of a new step for the group, Andrew Mines, of George Washington University’s programme on extremism labelled it “a direct confrontation with the Taliban”.
“It’s part of Isis’ branding campaign to really undermine the Taliban's credibility, not only to protect their own fighters and their own personnel but to protect civilian populations and especially vulnerable minority populations like the Hazaras, like the Shiites that we're seeing,” he told NPR.
Ahead of its first face-to-face talks with US officials since its takeover of Kabul, the Taliban insisted last week that it would not co-operate with Washington to contain the increasingly active extremist group.
“We are able to tackle Daesh independently,” Taliban spokesperson Suhail Shaheen told The Associated Press.
With its surveillance capabilities in Afghanistan greatly diminished, the US admitted last month that a drone strike meant to foil a suspected Isis-K threat to Kabul airport mistakenly killed 10 civilians.
Additional reporting by agencies
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