Shown as a teaser on the FHM website on Saturday, the cover featured a light-skinned, scantily clad local film actress stepping into the light from a a group of dark-skinned young women in black bikinis in the dim background.
The page carried the tagline, "Stepping Out of the Shadows."
"We deem this to be the most prudent move in the light of the confusion over the previous cover execution. We apologise and thank those who have raised their points," FHM said in a statement on its Philippine website.
"When FHM hits the stands in March it will have a different cover," it added, but feature the same actress, Bela Padilla.
Contacted on Tuesday, FHM Philippines staff told AFP its editors did not wish to add anything to the statement.
FHM Philippines was flooded with criticism on social networking sites, the majority apparently from incensed, brown-skinned Filipinos after the cover was posted online.
"Seriously, did you guys not sense how racist this concept was?" wrote a film student on the Facebook page of FHM Philippines.
"That some people including the editors did not find an issue with that ignorant FHM magazine cover shows how deeply ingrained racism is in Philippine society," a Filipino in the United States commented.
Another person commented on the microblogging site Twitter: "What do you expect??? Can you really expect some form of sensitivity from a magazine that prides itself in exploiting women for profit?"
Summit Media, the publisher of the magazine, boasts on its website that FHM Philippines is the number one men's magazine in the country with more than a million readers.
Source i saw the interview with the girl in it, and she is dumb. i don't get it. and some of the people who were in the shoot were some light skinned Filipino painted black. seriously, i can't. Watch the interview with the girl here