The action comes after Interior Minister Nisar Ali Khan suspended a re-admission agreement with the EU last month, alleging that it was being misused by some countries to send back people without proper verification.
The Federal Investigation Agency (FIA) stopped the 'unverified deportees' from disembarking the plane after it landed at the Benazir Bhutto International airport here earlier today.
The interior ministry said in a statement that Greek authorities had not provided proper documentation of the passengers on board the charter flight being Pakistani citizens and it would not allow them to enter the country if their citizenship could not be confirmed.
The deportees and the flight crew were initially not allowed to disembark the plane and later on 30 deportees were sent back on the same flight, while 19 were accepted as Pakistanis.
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Khan had a meeting with the EU migration commissioner in Islamabad last month and apparently they agreed to settle the row, as EU promised not to deport anyone to Pakistan without proper verification.
Earlier, the minister said that Pakistan could not allow any country to label its innocent citizens as terrorists and send them back.