Gunmen on Saturday shot dead 13 Hazaras after dragging them out of their vehicles in the usually tranquil northern Balkh province, in a rare fatal attack targeting ethnic minorities.
No group has so far claimed responsibility for the attack.
Observers say IS have struggled to gain a firm foothold in Afghanistan because of the lack of a deeply sectarian environment -- unlike Syria and Iraq where the group has captured large swathes of territory.
"These acts are being perpetrated to breed fault lines, intolerance and discrimination," the Taliban said referring to Saturday's attack, without naming IS.
"We strongly condemn this incident... (and) call on our nation to be vigilant of all enemy plots," said the statement posted on their website on Sunday.
IS has been trying for months to establish itself in Afghanistan's eastern badlands, challenging the Taliban on their own turf.
Its franchise in the war-torn country has managed to recruit some disaffected Taliban fighters, as the fractious Afghan militant movement wrestles with a bitter power transition.
But the loss of senior commanders in drone strikes and the group's signature brutality, which repels many Afghans, has helped stem its advance.
Frequent clashes and firefights with Taliban insurgents have also hampered its bid to capture significant territory.
The Taliban, who have themselves often been accused of savagery during their 14-year insurgency, are seeking to appear as a bulwark against IS's rein of brutality and as a legitimate group waging an Islamic war.
Earlier this month the Taliban condemned a "horrific" video that apparently showed IS fighters blowing up bound and blindfolded Afghan prisoners with explosives.
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