Shahzad, was charged on five counts, including attempting to use weapon of mass destruction.
During interrogation, Shahzad admitted having attended a militant training camp in Waziristan. He bought a sports utility vehicle that was found loaded with an improvised explosive device in Times Square.
Investigators said that the Connecticut resident has implicated himself and told them he was acting alone.
Interior Minister Rehman Malik said that Shahzad has a Karachi identification card although his family is from the Pabbi area in Khyber Pakhtunkhwa.
Two people thought to have been in contact with Shahzad, have also been detained in Karachi.