The Group B match was due to be played on October 10, having previously been scheduled for March 28 and June 8.
Hairmau Malaya who are handled by head coach Nelo Vingada was scheduled to meet North Korea on Oct 5 and Hong Kong on Oct 10.
"The Ministry of Foreign Affairs hereby informs the public that all Malaysians are banned from traveling to the Democratic People's Republic of Korea (North Korea) until further notice", a statement on the ministry's website reads.
Malaysia has traditionally maintained cordial ties with North Korea, despite the country being treated as an outcast state by much of the developed world.
Malaysia, one of the small number of countries that still have diplomatic ties with North Korea, said the travel ban will be reviewed "once the situation has returned to normal".
FAM general secretary Datuk Hamidin Mohd Amin said they had informed AFC that the national team would be unable to travel to Pyongyang due to the directive from the Foreign Ministry.
The news led to the match being postponed for a third time, with the Asian Football Confederation saying in a brief statement the situation would be "referred to the appropriate committees to decide on the future status of this match".
Malaysia is one of North Korea's few remaining diplomatic partners even though bilateral tensions escalated after North Korean leader Kim Jong-un's estranged half brother Kim Jong-nam was mysteriously killed at the Kuala Lumpur airport in February.
"AFC via Datuk Windsor in its letter of reply to FAM this evening had agreed to make a decision that a match between North Korea and Malaysia would not be played in Pyongyang on that date", he said.
"The travel ban covers all Malaysians, and as Malaysians, the Malaysian national football team is included too", Reezal told Reuters.