About 3 million Afghans have been living in Pakistan for decades. Nearly half of them are unregistered and staying in the country illegally.
The decision to extend the deadline for their return was taken by federal cabinet yesterday.
"The cabinet approved grant of 60 days extension in the Proof of Registration (PoR) cards for Afghan refugees," said the statement.
The validity of legal refugee status for many Afghan refugees expired on January 31. This threw into doubt the future of these refugees.
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The Pakistani government says the country's economy "has carried the burden of hosting Afghan refugees since long and in the present circumstances cannot sustain it further."
The 60-day extension came as Afghan Interior Minister Wais Ahmad Barmak and National Directorate of Security chief Mohamed Masoom Stanekzai visited Pakistan to discuss bilateral ties.
The security situation in Afghanistan, where US-led coalition forces and the Afghan army continue to battle the Afghan Taliban for control of areas of the country, has been deteriorating in recent weeks.
A day later, at least 11 soldiers were killed when gunmen attacked a military academy, also in Kabul.
Afghanistan and the US have blamed Pakistan for allegedly providing safe havens to elements of the Afghan Taliban and Haqqani Network. Pakistan denies the charge, alleging that it is Afghan forces that offer sanctuary to elements of the Pakistani Taliban.