The club members were attending an "iPod Shuffle Night" on Saturday night in which they were encouraged to dress as their favourite recording artists.
Pictures of members dressed as different African American singers attracted a storm of criticism, both online and from people such as Victorian Premier Daniel Andrews and Australian rapper Adam Briggs.
The outcry was compounded when someone from the club left an expletive-ridden voicemail message on Briggs' phone, in which an alleged member of club said: "We’re at a function where it’s called an iPod shuffle night and people come dressed as people and that’s what they f***ing do”.
Frankston Bombers president Chris Sharman also defended the club members' decision to dress in blackface to the Herald Sun.
However the club was eventually forced to issue a statement on Sunday afternoon apologising for "any offence" caused.
"We now understand that our actions at last night’s club event have caused offense and division and for this we apologise," the club said in a statement on Facebook.
"We are extremely regretful of the situation that has transpired over the last 24 hours and want to assure our supporters, sponsors and the wider community that the Club is in no way racist and unreservedly apologises for any offense that has been caused.
"The club is committing to put in place an educational program relating to vilification and discrimination with to ensure we learn from this and come out of it a better and more educated Club.
"The club has received many abusive and threatening communications in relation to the labelling, and being volunteers we acknowledge that we may not have responded in an appropriate manner to these abuses and threats and for this we unreservedly apologise."
Mr Andrews told the club needed "to have a look at themselves" and that the behaviour was "not in the spirit of football and not in the spirit of Victoria".
The pictures have since been deleted from the club's Instagram page and any mention of the function has been removed from its Facebook page.
However other pictures from the event, predominantly women, remain on the Instagram page.
The incident is reminiscent of a blackface scandal that engulfed the Australian Opals basketball team when player Liz Cambage publicly slammed teammate Alice Kunek for dressing in blackface and posting a photo on Instagram.
"I'm am so shocked and disturbed to see this behavior from someone I'm meant to call a 'teammate'," wrote Cambage, whose father is Nigerian.
"Blackface is disgusting, I honestly have no words."
- with AAP
