The latest strike also raised the possibility of a military escalation between nuclear-armed India and Pakistan that would wreck a 2003 Kashmir ceasefire.
Tensions are brewing between India and Pakistan. New Delhi said it carried out "surgical strikes" on militants preparing to infiltrate from Pakistan-administered Kashmir on Thursday morning. But Islamabad said it was an "illusion".
The latest incident could threaten the fragile 2003 Kashmir ceasefire between India and Pakistan and raised the possibility of military escalation between both nations that have nuclear arms.
New Delhi's claim follows its accusation that Pakistan was involved in the killing 18 soldiers in a pre-dawn attack on an army base in Indian-administered Kashmir earlier this month.
India said its strikes targeted "terrorists" who tried to infiltrate their border.
"The Indian army conducted surgical strikes last night at these launch pads," Lieutenant General Ranbir Singh, the director-general of military operations, said. "Significant casualties have been caused to these terrorists and those who are trying to support them. The operations aimed at neutralising the terrorists have since ceased," he told a press conference in New Delhi.
He did not say whether the strikes had been carried out by the Indian air force or by ground troops.
The top spokesman for the Pakistani military slammed the Indian account of its action as "totally baseless and completely a lie".
"We deny it. There is no such thing on the ground. There is just the incident of the firing last night, which we responded to," Director General of Pakistan Army's Inter-Services Public Relations, Lt General Asim Bajwa, told local news channels.
Pakistan's Prime Minister Nawaz Sharif vowed the military was capable of thwarting "any evil design to undermine the sovereignty of Pakistan."
There were no casualties or damage reported on the Indian side of the border but Pakistan reported that two of their soldiers were killed and nine were wounded in the attack.