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Indian home minister Sushilkumar Shinde said on Wednesday that Pakistan's Inter-Services Intelligence (ISI) agency was pressuring Sikh militant leaders to target Punjab and other parts of India.
"Pakistan rejects those remarks accusing us and implicating one of our government agencies for fomenting terror in Indian Punjab," said foreign ministry spokesman Aizaz Ahmad Chaudhry.
"Such a statement in our view is uncalled for and regrettable. We feel that making such statement has the potential of undermining the efforts made by both sides to normalise the relations between the two countries."
The Indian home minister had said that there had been "some significant development on the Sikh militancy front' and accused the ISI of seeking to further its "terror plans" in India.
Chaudhry urged Delhi to share any evidence it had of such involvement and said further accusations could harm already fragile ties.
Tens of thousands of people died in a separatist drive for a Sikh homeland which erupted early in the 1980s in Punjab, but the strength of the militancy has since waned.
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