What if marriage certificate is not available for passport application

My Sister got married to a Nepal guy. They do Christian Marriage in our hometown i.e. in Manipur and again court Marriage in Nepal. Now, both my sister and her husband want to apply for Work Visa in Canada and in this My sister is the primary applicant. The Embassy didn't accept their Court Marriage Certificate of Nepal. As my sister(Indian) is the primary applicant, they are told to register their certificate in India. So, my Question is.... Do they need to re-register their marriage in India and what is the process. I seek your wisdom and counsel in this. Thank you. I would be very glad to pay the fees as well. My sister and I are from Churachandpur, Manipur.