The Ministry of External Affairs said consular officials of the Indian High Commission were "harassed and denied access" to meet Indian pilgrims at Gurudwara Nankana Sahib and Gurudwara Sacha Sauda on November 21 and 22.
It said the access was denied despite the Pakistan Foreign Ministry granting them prior travel permission.
In a statement, the MEA said India has also expressed grave concern at the reports of attempts being made during the ongoing visit of the Indian pilgrims to Pakistan, "to incite communal disharmony and intolerance and promote secessionist tendencies with the objective of undermining India's sovereignty and territorial integrity".
There were reports that pro-Khalistani banners were shown to the Indian pilgrims in Pakistan.
It said Pakistan has been called upon to take all measures to not allow its territory to be used for any "hostile propaganda" and support for "secessionist tendencies" against India.