Authorities meanwhile revised the death toll from Wednesday's bombing in Kabul's neighborhood of Dasht-e-Barchi to 34 killed, not 48.
As family members and relatives were burying the victims in a mass grave on a hill overlooking Kabul, a group of armed men launched an attack on a training facility used by the country's intelligence agency in a different part of the city.
Live television footage showed humvees patrolling the empty streets while gunfire echoed and a helicopter circling above.
Scores of Taliban were also killed, according to Afghan officials.
Kabul hospitals were completely overwhelmed in the immediate aftermath of the attack as officials collected data on the casualties, leading to the confusion and the initial wrong toll.
The attack comes just hours after a suicide bomber detonated explosives inside an education centre in a predominantly Shia area of western Kabul, where students were studying for college entrance exams, killing at least 37 people.
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Afghan security forces have been engaged with Taliban militants in the provincial capital days after the offensive on the strategic city began.
The brief respite sparked hopes the truce could clear the way for talks to end the almost 17-year-old conflict.
"Today's direct attack on an English language class in Kabul, which killed or critically injured dozens of children aged between the ages of 16 and 18, is deplorable", the statement said.
Mattis added, he believes Afghan forces are building momentum for peace talks.
Analysts have suggested the Taliban may be trying to shore up its position before any potential negotiations by proving they can hit government installations at will.
Kabul police spokesman Hashmat Stanekzai said the attackers were firing rocket-propelled grenades and other weapons but it was unclear how many gunmen were involved.
Both the resurgent Taliban and an Islamic State affiliate in Afghanistan have targeted Shiites in the past, considering them to be heretics.
So far, the aid group has retrieved 270 bodies but there was no breakdown or indication how many were Afghan security troops, Taliban fighters or civilians.
It also showed how militants are still able to stage large-scale attacks, even in the heart of Kabul, and underscored the struggles of the Afghan forces to provide security and stability on their own.