Foreign Minister Hina Rabbani Khar had taken up the handing over of Faqir Mohammad during a phone conversation with her Afghan counterpart Zalmai Rassoul on Wednesday night but Afghan Foreign Ministry spokesman Janan Musazai ruled out his extradition.
The Taliban commander was captured by Afghan intelligence operatives in the eastern part of Afghanistan on Monday.
During a weekly news briefing yesterday, Pakistan Foreign Office spokesman Moazzam Khan had said: "We hope that he would be handed over to Pakistan as soon as possible because he has the blood of many innocent Pakistanis on his hands."
The Afghan government's investigation into the recent capture of Mohammad "is still ongoing", Afghan Foreign Ministry spokesman Musazai said.
In a statement, Musazai indicated the refusal might be a tit-for-tat move as Pakistan had rejected Afghanistan's request to hand over certain Afghan Taliban prisoners during a recent tripartite summit in London.
"During the recent tripartite meeting in London, the Afghan government requested the Pakistani government to return Afghan Taliban prisoners held by Pakistan to Afghanistan so that they could participate in and support Afghanistan's peace and reconciliation efforts," Musazai said.