An inquiry committee led by a Rear Admiral, which was instituted by the naval chief, has started its probe into the attack, Pakistan Navy spokesman Irfan-ul-Haq said.
Officials of the Federal Investigation Agency, air force, paramilitary Pakistan Rangers and police are part of the investigation.
Haq said the committee will present its report to the naval chief but did not give a timeframe for completing the inquiry.
The audacious attack, in which six terrorists sneaked into the PNS Mehran naval airbase late on Sunday night, has raised fears about the Pakistani Taliban''s ability to target highly sensitive and guarded military installations.
A spokesman for the Tehrik-e-Taliban Pakistan, which claimed responsibility for the attack, said the terrorists were helped by "local friends" in Karachi. The Taliban has also said the attack was meant to avenge the killing of Osama bin Laden in a US raid in Abbottabad on May 2.
Pakistani commandos yesterday regained control of PNS Mehran after a 16-hour standoff with the terrorists.
At least two of the attackers reportedly escaped while the others were killed or blew themselves up.