A case under section 420 of the IPC and section 42 of the Prisoners Act has been registered against Choudhary at the Cantonment police station.
The police will also probe whether Choudhary had been making phone calls to Pakistan.
Chaudhary, a native of Lahore, had been brought to the Amritsar central jail from Jalandhar three months ago. He had been booked under the Foreigners Act.