It is the first attack claimed by the terror network's new wing, whose creation was announced by chief Ayman al Zawahiri last week.
The claims, made on the anniversary of the 9/11 attacks in New York, will likely add to concerns about extremist infiltration of the Pakistani military's ranks after the Taliban, who also claimed to be behind the attack, said they received inside help.
Defence Minister Khawaja Asif had voiced concerns when addressing parliament on Wednesday, saying: "We cannot rule out the inside help in this attack because without it the miscreants could not breach security."
Al Qaeda in South Asia was launched last week in what experts see as a bid to remain relevant in the face of rising competition by the Islamic State (IS).
"The operation near Karachi shore was an attack by al Qaeda in the subcontinent," a statement in Urdu from the group sent to AFP said.
It claimed that the target of the raid was a "US supply ship" and said the dead attackers included former Pakistan Navy officers.
It was not immediately possible to confirm whether a US ship was present at the port. Militant groups in the region often exaggerate claims about attacks.
Commodore Nadeem Bukhari, a spokesman for the Pakistan Navy said an investigation into the attack was under way.
"It cannot be ruled out but it is still premature to say that it was an inside work," he told AFP.
Al Qaeda said the officers quit their jobs and joined the militants after growing becoming radicalised.
Al Qaeda was previously linked to a 2011 raid on another Karachi naval base that lasted 17 hours resulting in the deaths of 10 personnel and destruction of two US-made spy planes.
The new hardline Jamat-ul-Ahrar faction of the Pakistani Taliban sent a "greetings card" to journalists on Thursday gloating over the 9/11 attacks and hailing former al Qaeda chief Osama bin Laden.
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The murdered brave journalist Syed Saleem Shahzad, a citizen of Pak sought and spoke the truth about radicals among the Pak forces ranks. It was not an unfounded allegation. There was always a serious threat of defecting extremist traitors. But for some reason too sensitive for some twisted psychos, so-called 'national protectors' to disclose, who found a report that could help as something that 'harms national interest'. One would think
So these certain so-called insane 'national protectors' found a report that could be helpful as something that 'harms national-interest' than the actual threat within, which one would think is what harms 'national interest'. Instead they allegedly choose to kill Shahzad, a patriot, and show no good faith or priority in transparency on targeting treasonous terrorists, let alone previously acknowledging the problem while suffering these type of attackers.
These unaccounted 'non-extremist' criminals are still in service and sadly entrusted with security supposedly to 'protect the nation and its people'. They instead betray the public almost as bad as the extremist saboteurs, inflicting violence on defenseless investigators who only want to address major issues, but these certain watchmen fail to do so honestly.
India is responsible for this attack. This group doesn't exist. Its a PR stunt by Modi to target Indian Muslims and Kashmiris.
@Secure the borders: The south asian wing is led by a pakistani and has biggest participation from pakistanis alone. No doubt there are foreign fighters. But simply becuase there are some you want to extradite all afghans and bengalis and what not. Imagine if every country started extraditing all pakistanis because almost every where there is a pakistani connection to a terrorist attack or threat.
So the PN spokesman wants the world to believe that its still premature to say if PN officers were involved or not, 1 week after the attack? And that too when they claimed to have apprehended quite a few people during the attack?
Digraceful.
Can we please humanely repatriate all Afghan illegal immigrants (along with Uzbeks, Bengalis, Sri Lankans. Burmese etc).
Secure the borders. No other country would tolerate this. Leave the nihari alone for 5 minutes Mr Nawaz Sharif and concentrate on this please.
Consciously start a program to address the intolerance and extremism in our society.
We have had almost 4 decades of mullah rule now; it has been of no benefit to Pakistan or to Islam.