The altercation happened on a minor incident at a tea-stall and the district administration immediately intervened and arrested the accused, it said.
"Attempts to paint this incident as a communal issue are patently motivated. Most importantly, the gurdwara remains untouched and undamaged. All insinuations to the contrary, particularly the claims of acts of 'desecration and destruction' and desecration of the holy place, are not only false but also mischievous," the Foreign Office said.
The Foreign Office statement has come after some reports in the Indian media said that a mob attack had taken place at the shrine. The reports suggested that hundreds of angry residents at Nankana Sahib pelted stones at the Sikh pilgrims on Friday.
Police in Pakistan said on Friday that a group of people, led by the family of a Muslim man who married a Sikh teenager, held a day-long sit-in outside the gurdwara to protest the arrest of their relatives who were held for alleged forced conversion of the girl.
The External Affairs Ministry in New Delhi said on Friday that members of the minority Sikh community in Pakistan were subjected to acts of violence at the holy city of Nankana Sahib.
"India strongly condemns these wanton acts of destruction and desecration of the holy place. We call upon the government of Pakistan to take immediate steps to ensure safety, security, and welfare of the members of the Sikh community," the ministry said in a statement.
"Strong action must be taken against the miscreants who indulged in desecration of the holy Gurdwara and attacked members of the minority Sikh community," it said.
The ministry said reprehensible actions followed the forcible abduction and conversion of a Sikh girl who was kidnapped from her home in the city of Nankana Sahib in August last year. Gurdwara Nankana Sahib, also known as the Gurdwara Janam Asthan, is the site where the first Guru of the Sikhs, Guru Nanak, was born. It is regarded as one of the holiest Sikh sites.
The Pakistan Foreign Office said the Pakistan government was committed to upholding law and order and providing security and protection to the people, especially the minorities. It said the opening of the Kartarpur Corridor is a manifestation of Pakistan's special care extended to the minorities, in line with the vision of the the country's founder Muhammad Ali Jinnah.
Punjab Chief Minister Amarinder Singh and the Shiromani Akali Dal (SAD) had also expressed concern over reports of the mob attack on the Nankana Sahib gurdwara.
In a tweet, Singh appealed to Pakistan Prime Minister Imran Khan to ensure that the devotees stranded at the gurdwara were rescued from the mob. SAD chief Sukhbir Singh Badal urged Prime Minister Narendra Modi to take up the issue with his Pakistani counterpart.