It was the worst assault on a military base since the army headquarters was besieged in October 2009, piling further embarrassment on the armed forces three weeks after Osama bin Laden was found living under their noses.
Up to 20 militants crept into the base in the teeming port city of Karachi from three sides under the cover of night late Sunday, officials said, triggering gunbattles and a series of explosions.
More than 12 hours later, officials were unable to confirm that the attack on the PNS Mehran, a sprawling compound of the Pakistani navy's air arm, was over.
By mid-morning, fire crews had doused towering flames over the base.
Interior Minister Rehman Malik said the "terrorists" sneaked into the base from three points adjacent to residential areas in the city of 16 million people, whose port is a vital hub for NATO supplies bound for Afghanistan.
"A (single-storey) building in the premises is still under their occupation from where they are exchanging fire with our soldiers," Malik told reporters.
"It is not just an attack on a navy establishment, it is an attack on Pakistan," Malik added, warning that those who sympathise with the Taliban and Al-Qaeda should instead "join hands with us to save our country".
A spokesman for the Pakistani Taliban, who have stepped up attacks to avenge the May 2 death of bin Laden, said the militia had dispatched 15 to 20 suicide bombers equipped to fight for a week.
"We had already warned after Osama's martyrdom that we will carry out even bigger attacks," Taliban spokesman Ehsanullah Ehsan told AFP by telephone from an undisclosed location.
"Our people present inside are all fedayeen (suicide bombers). They are 15 to 20 in number and were sent after proper planning. They can fight for one week and until they embrace martyrdom," he said.
Bin Laden was killed by US commandos in a garrison town north of Islamabad, in a raid that humiliated Pakistan's security establishment. The militants' attack deep inside Karachi underlined the military's vulnerability.
An AFP reporter heard blasts and intermittent barrages of gunfire on Monday, and helicopters flying overhead. Dozens of ambulances queued outside the base, which is about 10 kilometres (six miles) from Karachi's international airport.
Farooq Bilal, spokesman for the paramilitary Rangers unit, told AFP that 11 navy officials and two paramilitary soldiers were killed in gunbattles with the militants. There were no confirmed casualties among the militants.
Navy spokesman Commander Salman Ali said one navy lieutenant and 10 sailors died from bullet wounds in clashes with the 10 to 15 attackers.
"They have destroyed two P-3C Orion aircraft," he added. The United States delivered the two maritime patrol aircraft to PNS Mehran only last June.
The attack was also likely to raise further concerns about the safety of Pakistan's nuclear weapons, which reportedly number more than 100.
The New York Times said that a mere 24 kilometres away from PNS Mehran, Pakistan was believed to keep a large depot for nuclear weapons that can be delivered from the air.
Ali told AFP that no foreigners were on the base at the time of the attack and said it was not thought to be a hostage situation.
Speaking to the ARY television station, Ali said: "The attackers first fired rockets. The terrorists also used small bombs and now they are firing with sophisticated weapons. They are inside and still resisting."
In October 2009, Taliban militants besieged the army headquarters in the garrison city of Rawalpindi for two days, killing 22 people and raising serious questions over why it took the military so long to put down the assault.
Karachi is Pakistan's financial capital and its port is used by NATO to ship supplies to the estimated 130,000 US-led foreign troops fighting the Taliban in neighbouring Afghanistan.
The assault was the fourth on the navy in Karachi in a month. Three bombings in late April killed nine people, including eight naval personnel.
Despite anger in Pakistan over bin Laden's killing, US President Barack Obama told the BBC he was ready to order a similar mission if another high-value target was discovered in Pakistan, or anywhere else.