"Never once in the history of FAM have we tried to build a Malay-dominated team," Redzuan Sheikh Ahmad said on Thursday.
"And we have never based our selection of players on race or religion. It's just unfortunate that the Indians and Chinese are not interested in football these days."
The country's Asian Cup squad, who finished bottom of Group C after failing to win a match, comprised 20 ethnic Malays and two Indians.
Malays make up about 60 per cent of the country's population, but Chinese and Indians are strong minorities in the country.
The FAM is preparing to explain to the government why the national team performed so badly at the Asian Cup.
The tournament's co-hosts conceded 12 goals in their three group games and scored only once.
In Singapore, ethnic Malays are the minority but make up more than 60 per cent of the national football squad.