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India said the Pakistani strikes in Afghanistan's Kunar and Paktika provinces violated regional peace and security.
MEA spokesperson Randhir Jaiswal expressed condolences for civilian lives lost and reaffirmed support for Afghan sovereignty.
Pakistan said its forces killed 28 terrorists in the border region.
The Afghan Taliban government said three civilians were killed and four were wounded.
Why it mattersThe condemnation could sharpen India-Pakistan tensions and affect regional security responses after strikes inside Afghanistan.
More context
The Taliban condemned the strikes as aggression and said Afghanistan's territory was not being used for attacks.