Until now, Pakistan has not confirmed Ajmal Kasab's nationality, saying he was not in the country's databases, reported the Associated Press.
Information Minister Sherry Rehman confirmed Kasab was a Pakistani in a text message but gave no further information, according to the AP.
Pakistani national security adviser Mahmud Ali Durrani told CNN that evidence India turned over to Pakistani authorities showed the gunman did have links to Pakistan.
The acknowledgement came after India turned over a 100-page dossier of what it said was evidence linking the Mumbai attackers to Pakistan.
Part of the dossier from New Delhi was transcripts of telephone calls that Indian authorities said they intercepted during the attacks.
The transcripts, obtained by the newspaper The Hindu, show the gunmen were in close contact with their handlers during the siege, the AP reported. India believes the handlers were senior members of Lashkar-e-Taiba, a Pakistan-based militant group.
The other nine gunmen were killed during the attacks.
Durrani said the information was useful to Pakistan's own investigation but was not enough, according to CNN.
"What the dossier is, is not something solid," he said. "But I would also say, some of the leads we got from India through other countries, that has been very helpful to our investigation."
Later Wednesday, Pakistani Prime Minister Yousuf Raza Gilani reportedly dismissed Durrani. The prime minister's office said he was fired "for his irresponsible behavior for not taking the prime minister and other stakeholders into confidence, and a lack of coordination on matters of national security."
Pakistani media reports indicated Durrani was fired for revealing the alleged Pakistani connections to the media without privately consulting the prime minister.
Ten gunmen killed 164 people during a three-day siege of India's financial capital in November. The attacks have heightened tensions between the two countries.