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The process is this way. You need to apply in Manipur ILP online portal website. You would find three kinds of permit, choosing accordingly, uploading the documents they have asked you submit the form. Fees payment links are provided too based on the type of permit. I personally feel once you have received the ILP you book your tickets. I have not travelled to Manipur, but few people I know travelled in July, through them I got the above info.
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I agree with you and have already done the same. but online payment is disabled. and also unable to check the status as the page is in development phase.