Welcome to the Wefugees Community and thank you for your question.
The platform and our experts are based in Germany. Therefore, we unfortunately may not be able to share much experience or knowledge with you on refugee regulations and procedures in Malaysia. I tried to make some research and read in various sources that Malaysia did not sign the Geneva Refugee Convention or its protocol. Malaysia does not seem to have established a comprehensive protection system yet and I am afraid that the government does not issue refugee passports (as far as I understood). UNHCR is registering asylum seekers and determine their status though, which I read here. UNHCR states:
"UNHCR identity documentation provides a level of protection which may reduce the risk of arrest, and allow limited access to health services, education and other essential support services from UNHCR, its partner organisations or other actors. This is only an identity document and has no formal legal value in Malaysia, neither is it a passport."
I also found an organisation called "asylum access Malaysia" - they offer support and legal counselling for refugees and are based in Kuala Lumpur. Please follow the link for more information and contact details.
I hope this helps and all the best,