The raid on the Jaish-e-Mohammad (JeM) camp was launched because India believed suicide attacks were "imminent", Foreign Secretary Vijay Gokhale told a media briefing.
"A very large number of Jaish-e-Mohammad terrorists, trainers, senior commanders and groups of jihadis who were being trained for fidayeen (suicide) action were eliminated," he said.
JeM, a Pakistan-based group, claimed responsibility for a February 14 suicide bomb attack in Kashmir that killed 40 Indian paramilitaries.
"Credible intelligence was received that JeM was attempting another suicide terror attack in various parts of the country, and the fidayeen jihadis were being trained for this purpose," said Gokhale.
"In the face of imminent danger, a preemptive strike became absolutely necessary. In an intelligence-led operation, in the early hours of today, India struck the biggest training camp of JeM in Balakot."
Pakistan had earlier said Indian warplanes crossed the ceasefire line in Kashmir and dropped payloads.
India regularly accuses Pakistan of supporting radical groups who stage operations in Indian-administered Kashmir.
The Himalayan region has been divided between India and Pakistan since the end of British colonial rule in sub-continent in 1947. They have fought two of their three wars over the region.
Pakistan denies supporting militants.
"The existence of such massive training facilities capable of training hundreds of jihadis could not have functioned without the knowledge of Pakistan authorities," said the foreign ministry official.
"India has been repeatedly urging Pakistan to take action against the JeM to prevent jihadis from being trained and armed inside Pakistan," he added.
"Pakistan has taken no concrete actions to dismantle the infrastructure of terrorism on its soil," he added.