"They have been told that this is unacceptable to us, and please put a stop to it," General Upendra Dwivedi told reporters in New Delhi in an annual briefing to the media.
Heads of military operations of both countries spoke to each other earlier on Tuesday, he said.
India's army reported sighting multiple drones flying over Indian-controlled border villages last week.
"These drones, I believe, were defensive drones, which want to come over (our territory) to see if any action is being planned against them," Dwivedi said.
There was no immediate response from Pakistan's army.
Muslim-majority Kashmir has been divided between India and Pakistan since their independence from British rule in 1947, and both claim the Himalayan territory in full.
The neighbours fought for four days in May 2025, weeks after New Delhi accused Islamabad of backing a deadly attack on tourists in Indian-administered Kashmir, claims Pakistan denied.
The ensuing conflict killed at least 70 people, and saw both sides make extensive use of drones as well as intense missile and artillery barrages.
"We are fully alert along the Line of Control," Dwivedi added, referring to the heavily fortified de facto border.
Dwivedi said several low-flying drones entered Indian-controlled airspace with their lights switched on -- as many as seven on Saturday, and another two or three on Sunday.
"It's possible they wanted to see if there were any gaps, laxity in our defence, any gaps through which they could send terrorists," he added.
Rebel groups in Indian-run Kashmir have waged an insurgency for 35 years demanding independence for the territory or its merger with Pakistan.
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