"I like Tony Abbott, I always have like him but on matters of politics we are on polar opposites", he said.
Macklemore responded to the controversy by saying he would "go harder" and "love" despite receiving "a lot of tweets from angry old white dudes in Australia".
It was also embraced by advocates for same-sex marriage around the world, particularly in the USA where same-sex marriage was being considered by several states and the Supreme Court.
The track, which was written with Ryan Lewis and Mary Lambert, hit number one on iTunes in Australia this week after former prime minister Tony Abbott argued "footy fans shouldn't be subjected to a politicised grand final".
"It is one of his most popular songs, and for Mr Abbott or anyone else to say that it should be banned I think is a weird thing to say".
Macklemore rehearsing ahead of Sunday's NRL Grand Final.
"Yo the NRL hooked me up, I got some Tim Tams, I got some Arnotts, I got some ANZACs, I got some koalas, some of these", the rapper said in the video.
The performance comes amidst the same-sex marriage postal survey, and vigorous campaigning from both sides of the debate in Australia.
Macklemore is determined to perform the song at the Grand Final.
MATT KING GETTY IMAGES Macklemore spread a message of equality at the NRL grand final
Responding to the controversy Thursday, Macklemore said on an USA radio show he was "going harder" in response to the anger around his performance.
The petition demands that the NRL "reconsider its political position and remove LBGTIQ politics out of the awesome sport of Rugby League".
But in an interview on The Project on Thursday night, Prime Minister Malcolm Turnbull laughed off concerns about Macklemore's performance.
"Don't use our dime and don't use our time to try and convince us of a political argument that you're putting", he said. "It is absolutely ridiculous", Senator Hanson told Channel Seven.
"That's one of his top songs, one of his hits".
A national survey on whether or not to allow same-sex marriage in Australia was mailed out to voters on September 12, kicking off a two-month campaign on the issue.
Regular opinion polls show the vast majority of Australians support same-sex marriage.