Foreign Minister Shah Mehmood Qureshi expressed disappointment over the sentence announced in Dr Aafia's case.
Speaking to CNN in New York, Qureshi said Dr Aafia has not been given the benefit of doubt and she reserves the right to appeal. He said the government will consult her family before it files an appeal.
About the government's role in this regard, Qureshi said that the Pakistan government had mobilised all resources at its disposal but it had limitations.
The sentence has sparked a reaction in the country as people took to streets on Friday to protest the decision.
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