Gender and Equality Commissioner Rowena Allen confirmed that she had accepted Ms Ward's decision to resign from the LGBTI Taskforce Education Reference Committee on Friday.

Ms Ward, meanwhile, issued a statement apologising for the comments. "They in no way reflect the views of Safe Schools Coalition Victoria or the Victorian Government," she said.

On Tuesday Victorian Premier Daniel Andrews apologised to the LGBTI community for past laws that criminalised homosexual behaviour and a rainbow flag was hoisted over Parliament House to mark the event.

According to a News Limited reports, Ms Ward posted a picture of the rainbow flag to her Facebook account with the words: "Now we just need to get rid of the racist Australian flag on top of state parliament and get a red one up there and my work is done".

Fairfax Media was unable to reach Ms Ward late on Friday evening to confirm her comments and clarify what they meant.

But her written statement said she apologised for any offence the comments may have caused the government and members of the LGBTI community.

"These were private comments that were never intended for the public domain," she said.

Ms Allen said the incident would not change the Victorian Government's "proud" support of the Safe Schools program.

"Ms Ward has acknowledged that the post was inappropriate and may have caused offence, even if meant in jest, and posted in private," Victoria's Gender and Equality Commissioner said.

"The Safe Schools program is not about any one person, it's about providing safe and inclusive environments for all LGBTI kids at school.

The program, which promotes acceptance of LGBTI people, has been regularly embroiled in controversy, with attacks from conservative MPs and Christian groups – some which have accused the program of promoting  "radical sexual experimentation" and  "encouraging cross dressing".