Mirza Nasir Baig, deputy commissioner in Thatta, said the pilgrims were on their way to a shrine fair when their boat capsized on the open sea near the coastal town of Bohara in Thatta.
The boat carrying members of the Dawoodi Bohra community capsized near to Thatta city.
There are conflicting reports on how the accident happened, how many boats were involved, and where it took place.
An annual festival to celebrate the birth anniversary of the saint was being held at the shrine.
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Different officials have placed the number of passengers on board between 50-100.
At least 21 bodies have been recovered, Dawn newspaper quoted officials at the Mirpur Sakro Taluqa Hospital as saying.
Most of the passengers were residents of Karachi, the police added.
The DC Thatta said that two boats with 60 people onboard struck to each other while going to Pir Pithu Mizaar due to strong winds.
Authorities fear a further rise in the death toll as search and rescue operations involving navy and coastguards are still underway, according to a statement from Pakistan Navy.
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