A navy officer and three attackers had been killed in the attack on the Karachi Dockyard in the port city of Karachi Sep 6 after militants breached the navy defence with inside help, Xinhua reported.
Pakistani Taliban and the newly launched Al Qaeda India branch had separately claimed responsibility for the attack.
The minister said security forces have arrested nine people, including navy officers, who have been arrested.
He said two officials of the Pakistan Navy, one commissioned and the other non-commissioned officer, who were also involved in the attack, have fled the country, probably to neighbouring Afghanistan.
Pak Taliban had separately claimed responsibility for the attack
"The fleeing navy officers were last located near the Afghanistan border," the minister told reporters at the parliament building in Islamabad.
He said there are evidences that outsiders were also involved in the attack, adding that scrutiny is being held to find out such elements in the security forces and the threats will be eliminated soon.
The security forces last week arrested three navy officers in the southwestern Quetta city who were trying to flee the country. One former naval officer who was expelled from the Navy in 2013 was also found involved in this incident. He was killed in exchange of fire.
The attackers, some wearing suicide jackets, had planned to capture a Pakistani ship, and to destroy an American ship in the sea.