Indian authorities had raised the issue with the Pakistan foreign ministry sough its help in tracing their missing citizens, Indian news agency ANI reported on Thursday.
Amidst reports that the duo had been detained by Pakistani Intelligence agencies, foreign minister Sushma Swaraj used Twitter to announce that she had taken up the matter with the Pakistan government.
Islamic militants in Pakistan have repeatedly targeted the followers of Sufi orders and their shrines, which extremists view as un-Islamic.
However, the Pakistan Foreign Office on Friday said that it had no information about the two missing men.
The minister stated that both Syed Asif Nizami and his nephew Nazim Nizami went missing after they landed at Karachi airport and Pakistan government has been requested for an update on both the Indian nationals.
"On 14 March, they offered another chadar at Data Darbar Sufi shrine in Lahore".
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Independently, Indian officials confirmed that Syed's sister had once had links to the MQM, one of Sindh's most powerful political parties - but also an organisation vilified by Pakistan's establishment.
"We appeal to the Indian government to get to know about the whereabouts of both". Nazim Ali Nizami was stopped to clear some documentation at Lahore airport and Asif Nizami was asked to board the flight.
Pakistani media continues to maintain radio silence on the disappearance of the two Sufi clerics from New Delhi's Nizamuddin Dargah.
India has taken up the matter seriously with Pakistan. According to reports, the 80-year-old and his nephew visited Lahore's Daata Darbar shrine and were supposed to fly back to India from Karachi on Wednesday.
Senior journalist and commentator Sultan Hali told National Herald that it seemed highly improbable that state agencies would detain such well-known and important visitors to Pakistan.