India's top counter-terrorism agency on Monday charged Jaish-i-Mohammed (JeM) and its leader Masood Azhar with perpetrating a deadly attack on the Pathankot air force base in January this year.

The National Investigation Agency (NIA) alleged that all four gunmen who stormed the air base on Jan 2 were "Pakistani nationals" and that Masood Azhar, the top leader of JeM, was the mastermind behind the attack.

"All the terrorists are accused of waging war against India. This was a criminal conspiracy to attack our security infrastructure," said a senior official at the NIA in New Delhi.

The presentation of a charge-sheet to a trial court wraps up India's investigation into the 18-hour siege at the Pathankot air base in which seven Indian security personnel and the four assailants were killed.

The attack, which came a week after Indian Prime Minister Narendra Modi paid a 'surprise' visit to Prime Minister Nawaz Sharif on the occasion of his granddaughter's wedding in Lahore last year, derailed a tentative thaw between the nuclear-armed rivals.

A joint investigation into the attack went nowhere and tension between the neighbours has risen over the course of a year marked by protests and cross-border clashes in India-held Kashmir.

Investigators in New Delhi said the charge-sheet and evidence would be offered to Pakistani authorities to take action against the perpetrators of the attack.

"We want Pakistan to arrest Maulana Masood Azhar and he should be deported to India," said a senior Indian home ministry official who is overseeing the investigation.

The charge-sheet cited DNA samples, food packets from Pakistan found in woodlands near the air base, a walkie-talkie set and a note found in a car used by the militants to drive to the base.

India said it had earlier given what it called "actionable intelligence" on alleged Jaish involvement in the attack to Pakistan, including telephone intercepts.

Pakistan took Azhar, who was also blamed for a 2001 attack on India's parliament, into 'protective custody' after the Pathankot attack.

Its investigators later found no evidence against either Azhar or Jaish-i-Mohammed.