The refugee card "protects against risks such as extortion, arbitrary arrest and detention as well as deportation under Pakistan's Foreigner's Act," spokesperson for the UN High Commissioner for Refugees, Adrian Edwards said in a statement.
Under the two-phase process, current card holders of the proof-of-registration (PoR) cards will get a replacement card valid till 2015 end.
The current cards are set to expire in June.
In addition, under the initiative, another 330,000 Afghan children below the age of 18 will receive birth certificates for the first time.
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Edwards said the UN agency "welcomes the issuance of birth certificates," adding that it offers important protection for refugee children as it helps to prevents statelessness, makes it easier for children to access social services and schooling, and allows for the issuance of documentation.
Last year, Pakistan had announced that it would renew its commitment to continue to provide protection and safety to Afghan refugees.
Since 2002, the UNHCR's voluntary repatriation programme has helped nearly 4.8 million Afghans return home from Pakistan and Iran after they fled their homeland during the Soviet war in Afghanistan in the 1980s.
The UN agency also supports the sustainable reintegration of Afghans who decide to return to their country.