Mullah Abdul Ghani Baradar, a powerful Taliban military chief who has been described as the militia's second in command, was arrested in Karachi.
The Afghan government and the former UN envoy to Afghanistan said his detention had adversely affected efforts to talk to the insurgents.
"The issue of prisoners is under discussion between the two countries," foreign ministry spokesman Moazzam Ahmad Khan told reporters when asked to comment on Afghan demands for access to Baradar and for his release.
The spokesman did not name any prisoner or give further details, but when asked, confirmed that Baradar was still in Pakistani custody.
Baradar is the most important Taliban leader to be captured since the 2001 US-led invasion ousted the Afghan militia from power in Kabul.
He was known as a trusted aide to the Taliban's elusive leader Mullah Mohammad Omar.
Shortly after Baradar's arrest, the Pentagon said two other Taliban officials were arrested, also understood to have been captured in Pakistan.
In March 2010, Kai Eide, the then just retired UN envoy to Afghanistan, said the arrest of key Taliban in Pakistan had stopped a secret channel of communication between the insurgents and the United Nations.
Afghan President Hamid Karzai has repeatedly invited the Taliban to open direct talks with his government and on Pakistan to facilitate an end to the 10-year war.
Pakistan has said it will do anything required by Kabul to support an Afghan-led peace process, but there is a wide degree of scepticism in Afghanistan and the United States about the sincerity of the former Taliban ally.
Correction: The picture caption in an earlier version of this article misspelled Mullah Baradar's name. The error is regretted.
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If the captured man were Mullah Abdul Ghani Baradar, a powerful Taliban military chief, why didn't the Haqqani fighters pressed for his release? After all Baradar was second in command and a trusted aide to the Taliban’s elusive leader Mullah Mohammad Omar!
Good bilateral relations between Pakistan and Afghan/taliban are essential for bringing the Taliban to the negotiation table. Release of prisoners from both sides will be first step toward delightful relations between the stake holders of the region.
Secrecy is paramount only a tiny group of insider on both sides privy to the Taliban.
It's Mullah Baradar, not Mullah "Baradari", in the caption to the picture above.