The coordinated attacks on hotels, hospitals and railway stations in Mumbai killed more than 160 people.
Malik, speaking to reporters, said Pakistani authorities had charged eight people with providing the Mumbai attackers with cell phones and helping them reach the city's shore by boats from Pakistan. Among them is the mastermind, a man who lived in a rented apartment in the city of Karachi.
"The incident has happened in India and part of the conspiracy has been done in Pakistan and therefore (the charge) will be aiding terrorism," Malik said.
Of the eight people charged, six are in custody, including a person from Barcelona, Spain, who Malik said made payments for the attackers' cellphone communications.
Malik said Pakistan would ask for Interpol assistance because the e-mail addresses and calling technology that the plotters used to interact with one another were registered in various countries, such as the United States and Italy.
"It worries me that somebody sitting in Pakistan and India were able to exploit the system in Italy and Spain to their benefit," he said.
The Indian government has said the three-day siege in Mumbai in November was carried out by Lakshar-e-Tayyiba, a Pakistan-based outfit. Malik agreed that some of the suspects have been linked to the organization.
The accusations renewed tensions between South Asia's longtime rivals, who have fought three wars since independence and conducted tit-for-tat nuclear weapons tests in 1998.
Pakistani officials promised to cooperate with the investigation, but insisted that India show evidence supporting the claims.
Announcing the arrests Thursday, Malik said: "People of India, we are with you and we have proved that we are with you."
Malik said the final report into the inquiry is pending and asked Indian authorities to help answer 30 questions, including providing the DNA of the suspects, that will help strengthen Pakistan's criminal case.
"We have a joint responsibility. We want to investigate. We just need help. And when we say 'help,' I am just signifying that we need more evidence," he said.
Previously, the only senior Pakistani official to acknowledge a Pakistani link to the attack was fired.
National Security Adviser Mahmud Ali Durrani was sacked on January 7 when he said that Mohammed Ajmal Kasab, the only surviving suspect from the attacks, had ties to Pakistan.