The three, initially detained at Sonamarg by the Jammu and Kashmir Police and later arrested, were identified as Sen, Debani Mukherjee, a director, and Arvind Singh Chouhan, who looked after the company's operations in Jharkhand.
"We have arrested them," IGP (Kashmir) Abdul Gani Mir said in Srinagar.
They will be produced in court tomorrow and taken to Kolkata on transit remand.
A Scorpio vehicle with a West Bengal registration in which they were travelling was seized.
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In Kolkata, Bidhannagar Police Commissioner Rajeev Kumar told reporters "a police team from West Bengal verified the identities of the three and they were arrested."
West Bengal Chief Minister Mamata Banerjee, who had earlier ordered Sen's arrest and indicated he was somewhere in North India, confirmed the arrest.
"Their identities have been confirmed and the entire credit for the arrest goes to the police," she said.
Police sources said the three had set out from the Salt Lake residence of Sen in Kolkata on April 12 in the Scorpio.
Since their vehicle bore West Bengal registration they were detained on suspicion by the Jammu and Kashmir Police and the West Bengal Police were informed, they said.