"I think it's clear to everyone to see that making her a Companion of the Order of Australia has nothing to do with tennis", he said on Twitter.
The award is to recognize Court's "eminent service to tennis" as victor of a record 24 Grand Slam singles titles and a mentor for young athletes.
"I strongly support a freedom of religion and I support respecting people's religious views, but I would invite Ms Court to reflect on the fact that her views and the ways she has expressed them has not always been respectful to other Australians, have caused great hurt and anguish for many, many Australians and in my very strong view have not reflected mutual respect and respect for people's beliefs and respect for people's sexuality that is an important part of being a modern Australian".
Victorian Premier Daniel Andrews hit out at the decision to honour Ms Court, saying she did not exhibit the values or hold the attitudes supported by the majority of Victorians.
Yesterday LGBTI rights organisation just.equal highlighted some of the comments that Reverend Court has said over the last two decades.
"All my life I've had those views and I was just saying what the Bible says", she said.
"I should always be able to say my views biblically, being a pastor and helping people with marriages and family".
Views on Court have changed since her playing days on the tennis courts.
'I have nothing against people - I love the people. We have them come into our community services, all kinds - whether they're gay, transgender, whatever they are.
'We never turn a person away and I think it's been tried to be made out that I'm somebody that I'm not really.
"I think they've been an worldwide embarrassment and belong in a very different era".
Prime Minister Scott Morrison didn't comment on Court's honor.
"It is a system that recognises the full spectrum of individuals across this country", Morrison said of the awards. It is an announcement that will be announced on that day.
Federal Labor has questioned why Court was given the top honour when she had already been recognised for her sporting prowess with an Order of Australia membership.
Margaret Court looks on during a Tennis Hall of Fame ceremony on day nine of the 2020 Australian Open at Melbourne Park on 28 January, 2020 in Melbourne, Australia. "I'm sick of having this discussion in one form or another, every single summer". Her criticisms sparked calls for Australia to rename the Margaret Court Arena, which is one of the venues for the annual Australian Open.
Smith said despite Court's "giant achievements in tennis", honouring her with a Companion in the General Division would "puts "humanity at large" and "Australia in reverse".