They opened fire near the village of Churunda, near the Line of Control that acts as the de facto border in the Kashmir region, according to the Indian statement.
Government officials in Islamabad were not immediately available for comment.
"Pakistani troops... started firing heavy-calibre weapons on the houses of civilians of Churunda village resulting in the death of three civilians," the statement said.
Local residents have reported sporadic small-arms exchanges between Indian and Pakistani troops in the same sector for the past fortnight.
Correction: In an earlier version of this article, Indian-administered Kashmir was mentioned as Indian Kashmir. The error is regretted.
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