Senior Army officials said that the training activity was organised, supervised and monitored in the area under the 9 Corps of the Indian Army.
The comments by External Affairs Ministry Spokesperson Arindam Bagchi came when asked about the decision by the Financial Action Task Force to retain Pakistan on its "grey list".
Patrolling has been strengthened near sensitive areas in and around Pathankot and additional forces have been deployed.
A joint search operation was being conducted in the area by the BSF and the Punjab Police, a police official said.
The Jammu and Kashmir's elite Crime Branch will produce the charge sheet in the case as well as all the accused in the case before the district and sessions judge in Pathankot.
Trial in Kathua rape and murder case moved to Pathankot court; girl’s family welcomes the move; accused to file fresh petition in Supreme Court.
The film Uri, Ronnie Screwvala's production company RSVP, is to be directed by Adia Dhar and will star actor Vicky Kaushal as a commando, who leads a group of paratroopers across the border.
2016 proved to be a tough year for the Punjab government with the apex court ruling on the vexed Sutlej Yamuna Link issue.
The reaction comes after NIA filing a charge sheet yesterday against Jaish-e-Mohammed (JeM) chief Masood Azhar in the Pathankot attack.
The ministry may now ask the channel to be taken off air for a day on November 9.
India blamed the raid at Pathankot in Punjab state on a Pakistan-based militant group that also staged a 2001 attack.