Eleven pilgrimage centres have been selected in the first phase of the scheme which is open to 25,000 applicants.
Applicants have to fill up a form available at all divisional headquarters in the state with the last date for submission of the same being July 1.
In case the number of applicants exceeds 25,000, a lottery would be done to identify the final beneficiaries, officials said.
"Special trains will be available at each divisional headquarters to ferry 1,000 people at a time. Medical services along with one attendant will be there in each coach," an IRCTC official said after the signing of the MoU.
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Arrangements for meals, accommodation and road travel would be made by the IRCTC for those availing the scheme.
People above 65 years of age will be allowed to take an attendant with them while the state government will provide an attendant for every group of 25 people.
Puri, Gaya, Rameswaram, Vaishno Devi, Tirupati, Varanasi, Amritsar, Dwarkapuri, Bihar Sharif, Shirdi are among the pilgrim destinations covered under the scheme.