The showpiece match will now be played at the Shah Alam Stadium in Selangor, some 25 kilometres west of the capital.
The switch marks the second consecutive year that the 80,000-capacity Shah Alam venue will stand in for the National Stadium. Last year, it was due to maintenance work being carried out on the track around the pitch.
It appears local officials prioritise the lucrative pre-season matches involving Premier League teams, which pass without incident, over domestic matches.
"The plan was to hold the Malaysia Cup final at the National Stadium because it's a neutral venue and the biggest stadium in the country," Malaysian Football Association official Hamidin Mohd Amin told local reporters.
"However, we received an update on the pitch conditions... and found that it won't be ready.
"The grass is new and the pitch is not fully even yet. This poses a safety risk to the players. We have no choice but to hold the final at the next biggest venue in the country."
The final is scheduled for Oct. 20 and will feature the winner of Kelantan and Selangor, versus either Armed Forces or Singapore's Lions XII.
The venue switch is a boost for Selangor, who play their home matches at the Shah Alam stadium.