A group of about 25 separatists were airlifted to Agra from Srinagar on Thursday, officials said.
The group consists of mainly "potential stone pelters" who have a history of trouble-making.
They are alleged to be active members of separatist groups in Kashmir Valley.
They were taken in a special IAF plane to Uttar Pradesh and lodged in Agra Central Jail.
The government has imposed strict restrictions in Jammu and Kashmir after the constitutional provisions that accorded the state special status were abrogated and it was divided into two union territories.
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