"From our initial observations, if such an incident took place, it would have involved a small section of spectators at the match and this surely does not reflect the feelings of the majority of fans in this football loving country," it said in a statement.
The qualified apology comes after the FA of Malaysia received a complaint from Chelsea over alleged racist abuse targeted at Benayoun during a friendly match with the Malaysian XI in Kuala Lumpur on July 21.
The midfielder was booed and jeered whenever he touched the ball in the 1-0 win against Malaysia in the capital of the Muslim-majority country.
Benayoun was the first Israeli to play in Malaysia, which strongly supports the Palestinians and does not recognise Israel, maintaining no diplomatic ties with the country. Some 60 percent of Malaysia's population is Muslim.
A statement on Chelsea's website read: "Notwithstanding most fans behaving appropriately on the night, we believe Yossi was subjected to anti-Semitic abuse by a number of supporters at the game.
"Such behaviour is offensive, totally unacceptable and has no place in football.
"The club did not make representations at the time as it was initially unclear as to the nature of the abuse Yossi received, as several players from both teams experienced similar treatment, sometimes louder and longer.
"However, having taken time to consider the issue fully, it has become apparent that a formal complaint was necessary."