At least five attackers and seven Indian soldiers have died so far. It is unclear how many militants are still inside the base.
Indian PM Narendra Modi held a meeting on Sunday to review the situation.
The attack is being seen as a blow to an apparent Indo-Pakistani peace initiative launched just days ago.
Hopes for a thaw in relations were raised after Mr Modi paid an unexpected visit to his Pakistani counterpart, Nawaz Sharif.
Pakistan`s foreign ministry and the US State Department have condemned the attack.
The attack started before dawn on Saturday, when a group of gunmen - wearing Indian army uniforms - entered the residential quarters on the base.
Hours of heavy gunfire followed, and a helicopter was seen firing at the facility on Sunday.
The identity of the attackers is not clear. Some Indian security officials suggested the Islamist militant group Jaish-e-Mohammed was to blame.
India says the group is backed by Pakistan, but Islamabad denies this.
In July seven people were killed in a similar attack when gunmen stormed a police station in nearby Gurdaspur district. The three attackers in Gurdaspur were killed after a 12-hour standoff with police.
Pathankot air force base is about 430km (270 miles) north of the Indian capital, Delhi and is on the road linking Indian-administered Kashmir with the rest of the country.
Indian-administered Kashmir has seen a long-running insurgency against rule from Delhi, and Kashmir has been a flashpoint in relations between Pakistan and India for nearly 70 years since independence.
More about:
