Al-Jazeera reports that Karzai met with Sirajuddin Haqqani, who was accompanied by top Pakistani military and intelligence officials.
The Haqqani network has alleged ties to Pakistani and U.S. intelligence networks stemming from the involvement in Afghanistan that followed the withdrawal of Soviet forces in the 1980s.
A spokesman for the Afghan president denied the talks and Pakistani army spokesman Maj. Gen. Athar Abbas told al-Jazeera that he had "no knowledge of such a meeting taking place."
Karzai during his May visit to Washington outlined his plans for a reconciliation and reintegration program that included bringing moderate insurgent elements into the political process.
CIA Director Leon Panetta during a weekend interview with ABC News said he doubted members of the Haqqani network were interested in the peace process, however.
"We have seen no evidence that they are truly interested in reconciliation where they would surrender their arms, where they would denounce al-Qaida, where they would really try to become part of that society," he said.
Al-Jazeera correspondents said with the Washington war plan in Afghanistan under scrutiny amid plans to withdraw combat forces as early June 2011, Karzai may be "cozying up" to his neighbors in Pakistan in his talk with regional militants.
The militant Haqqani network was linked to a Jan. 18 attack in Kabul that coincided with Karzai's inauguration of his new Cabinet ministers