Hussain was set to be hanged tomorrow morning in the central jail for the kidnapping and murder of a seven-year-old boy in an apartment building of Karachi where he worked as a security guard.
President Hussain ordered the postponement of Shafqat's hanging, media reports said.
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"We have learnt from multiple sources that Shafqat's execution has been stayed. We have yet to see an official notification but personally handed over his mercy petition to an official of Presidency at 11:30pm (Wednesday)," Communication Specialist for Justice Project Pakistan Shahab Siddiqi said.
The project is fighting for Shafqat's execution to be stayed. Shafqat was 15 when he was convicted in 2004.
His case has attracted attention as he was awarded the death sentence by the court when he was a juvenile and rights campaigners complain he did not get a fair trial and was only 15 at the time of the killing.
His mother, Makhni Begum, had earlier said in an interview that the police had shown the age of Shafqat as 20 at the time of his sentencing since he did not have any verified documents and the defense lawyer also did not object.
Shafqat's death warrant was issued earlier this month by an anti-terrorism court and the Sindh High Court also threw out a petition seeking suspension of his fresh execution order.
Makhni Begum this week also filed a mercy petition with the President.
A jail official, who was waiting for official order for staying Shafqat's execution, said that it had likely been postponed.
But a Sindh government official said they were yet to receive any orders from the Presidency staying the execution.
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