The Hindus were told by immigration officials that they could not cross the border despite having valid visas as they did not have "security clearance," sources told PTI.
The immigration authorities had reportedly received directions from the Interior Ministry not to let any Hindu go to India even for pilgrimage, the sources said.
The Hindu families reached Wagah at 8 am but most of them were not given clearance to cross the border till noon. Only two families from Karachi that had "no objection certificates" were allowed to cross over to India, the sources said.
However, Federal Investigation Agency official Waqar Haider told PTI in Lahore that his organisation was not stopping anyone possessing valid travel documents from going to India.
The kidnapping of a teenage Hindu girl, Manisha Kumari, from Jacobabad city of Sindh province on Aug 7 has caused widespread concern in the minority community amidst reports of an exodus of some 250 Hindus from the region.
Hindus from Sindh and Balochistan had decided to migrate to India because of forced conversions, extortion and kidnapping, TV channels reported.
The Hindus were travelling to India on 30-day visas for a pilgrimage to Haridwar and Vaishno Devi but many were not expected to return, the channels reported.
Taking notice of these reports, Interior Minister Rehman Malik yesterday said the Hindus would be stopped from going to India. He said they would be allowed to travel only after a probe by the FIA.
Malik claimed the reports of the migration of the Hindus were part of a "conspiracy to defame Pakistan." The Indian High Commission should explain why visas were issued to the 250 Hindus, he said.
Reports from Jacobabad said seven Hindu families comprising 90 people had yesterday left for Lahore to travel to India.
"We are businessmen but have been compelled to leave our motherland because of harassment, lawlessness, looting, kidnapping of girls and their forced conversion to Islam," said Amesh Kumar of Bakhshapur area in Jacobabad.
Another unnamed Hindu man from Quetta told the Dawn newspaper: "Pakistan is our homeland and at the moment we are going to India for visiting our sacred places. But if I find the situation in India better than in Pakistan, I will prefer to settle there and others also think the same way."
There were also reports that 52 Hindu families from Jacobabad had migrated to India about six months ago. Sindh Chief Minister Qaim Ali Shah too took notice of the reports of the migration of Hindus and formed a three-member committee of provincial ministers to assess the situation in Jacobabad and submit a report.