The attack on the high security facility took place on Saturday but it was kept under wraps due to strategic reasons, a naval spokesman said.
At least six militants tried to storm the facility on Saturday but the attempt was foiled by marine and army commandos who killed two militants and captured four others, the spokesman said.
The dockyard located in West Wharf is used for repairing the navy warships and submarines.
A security source said that the target of the attackers were Pakistan naval ships in the dockyard.
The Pakistani Taliban has claimed responsibility for the attack and said that it had the help of insiders in carrying out the terror strike.
It was the fourth major attack of the year on sensitive areas after militant's attack at airports of Karachi and Peshawar and botched storming efforts at two airbases in Quetta.
In the offensive launched in mid-June, Pakistan's army has killed more than 900 militants and lost 82 soldiers.
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