At least four navy personnel were killed and nine wounded in fighting at the Naval Station Mehran that was going on more than four hours after the strike began, said navy spokesman Irfan ul Haq.
He did not know how many militants had been killed or wounded.
Between 10 and 15 attackers entered the high-security facility before splitting up into smaller groups, setting off explosions and hiding in the sprawling facility, he said.
"We are receiving fire from different directions," said another spokesman, Salman Ali.
The coordinated strike rocked the country's largest city just under three weeks after the death of Osama bin Laden in an American raid on the northwestern garrison city of Abbottabad, an event al-Qaida allied extremists here have vowed to avenge.
The unilateral American raid triggered a strong backlash against Washington, which is trying to support Pakistan in its fight against militants.
The fact that militants were able to enter one of the country's largest military bases is another embarrassing blow to the army and will raise questions over whether the attackers had inside information. That they targeted a U.S. supplied aircraft draws attention to American aid to the military, something generals here do not talk about, fearing criticism from the county's fiercely anti-American population.
After heavy American prodding, security forces launched several operations against militants in their heartland close to the border with Afghanistan over the last three years. The extremists have struck back against police and army targets around the country.
No group claimed responsibility for the attack. But the Pakistani Taliban, an al-Qaida allied network which has previously launched attacks in Karachi, has pledged to retaliate for the death of bin Laden, and has claimed responsibility for several bloody attacks since then.
Pakistani Prime Minister Yousuf Raza Gilani condemned the attack, saying such a "cowardly act of terror could not deter the commitment of the government and people of Pakistan to fight terrorism."
Sunday's raid appeared to be the most serious against the military since October 2009, when militants attacked the army headquarters close to the capital, Islamabad. They held dozens hostage in a 22-hour standoff that left 23 people dead, including nine militants.