Locked in a longstanding dispute over Kashmir, the two countries have engaged in daily clashes since Wednesday when India launched strikes inside Pakistan on what it called militant bases. Pakistan vowed to retaliate.
"India through its planes, launched air to surface missiles ... Nur Khan base, Mureed base, and Shorkot base were made targets," Pakistan military spokesman Lieutenant General Ahmed Sharif Chaudhry said late on Saturday.
One of the air bases is in the garrison city of Rawalpindi, which just outside the capital Islamabad, and the other two are in Pakistan's eastern province of Punjab, which neighbours India.
Chaudhry said only a few missiles made it past air defences, and those did not hit any "air assets," according to initial damage assessments.
India's defence and foreign ministries did not immediately respond to a request for comment outside regular business hours.
India said its strikes on Wednesday were retaliation for a deadly attack on Hindu tourists in Indian Kashmir in April.
Pakistan denied India's accusations that it was involved in the tourist attack. Since Wednesday, the two countries have exchanged cross-border fire and shelling, and they have sent drones and missiles into each other's airspace.
Much of the fighting on Friday was in Indian Kashmir and neighbouring Indian states. India said it shot down Pakistani drones.
At least 48 people have been killed since Wednesday, according to casualty estimates on both sides of the border that have not been independently verified.Â
Meanwhile, residents across Pakistan and India have rushed to stockpile food and other essential supplies while families living near the border flee to safer areas, as armed clashes between the nuclear-armed nations escalate.
In the Pakistani city of Lahore, which lies near the border, residents were shaken on Thursday by drones that Pakistan said were launched by India and were shot down in the city, setting off sirens and leading the US consulate to tell its staff to shelter in place.
Schools were closed on Friday and residents and shopkeepers said Lahoris were stocking up on food, gas cylinders for cooking and medicine, prompting authorities to issue a notice warning businesses not to artificially increase prices.
India responded with drones on targets in Pakistan and destroyed one air defence system, Indian Air Force officer Vyomika Singh told a media briefing.
Pakistan Information Minister Attaullah Tarar had dismissed earlier Indian accusations of Pakistani attacks as "baseless and misleading" and said Pakistan had not carried out any "offensive actions".
In Pakistani Kashmir, officials said heavy shelling from across the border killed five civilians, including an infant, and wounded 29 others in the early hours of Friday.
The fighting is the deadliest since a limited conflict between the two countries in Kashmir's Kargil region in 1999.
Sirens blared for more than two hours earlier on Friday in Amritsar, which houses the Golden Temple revered by Sikhs.
Tourists fled the city by road as the airport was closed.
Further south in Bhuj in Gujarat, authorities said tourist buses were on standby in case they needed to evacuate people near the Pakistan border.
