The MM2H Office has just announced (5 October 2020) that applications to re-enter Malaysia from abroad for MM2H recipients stranded overseas has been shifted more directly to the Ministry of Immigration. Permission is no longer required of BOTH Ministries.
http://www.mm2h.gov.my/dms/uploads/6757-[UPDATED]%205%20OCTOBER%202020%20CURRENT%20GUIDELINES%20ON%20THE%20RE-ENTRY%20OF%20MM2H%20PARTICIPANTS%20INTO%20MALAYSIA%20DURING%20RECOVERY%20MOVEMENT%20CONTROL%20ORDER%20(RMCO).pdf
It appears that no travellers coming directly from or recently who have been resident in 24 countries (listed in the application) will be permitted.
Other travellers should be aware they face a 14 Day Quarantine and series of Covid testing and shall be liable for the full cost of accommodation, meals, and administration of the tests (RM4700).