Pastor Russell Embling said the Lighthouse Church was "an evangelical church holding to traditional Biblical values regarding marriage and the family".
Mr Embling said they would honour the commitment for the concert to take place, but Mr Rogers and Moa's manager decided to go to another venue.
Comments posted on the Wairarapa Times-Age website and social media sites showed support for the singer.
Amanda Sim wrote on Facebook: "When it comes down to it she's a 'singer' (and an amazing one at that) ... Does it matter who she loves?"
On times-age.co.nz, Ricky Rogers wrote: "I'm off to get my tickets for this now, if for no other reason than to support St Marks for being better people and to show I really don't like this type of discrimination in my town."
Comments also backed St Mark's Church welcoming Moa.
One Masterton reader wrote: "Good on you Staint Marks Church ... Lighthouse, you missed out on an amazing opportunity!!" Linda Reed wrote: "Go Carterton another great local event for town."
Another comment said: "Everyone is allowed to have their own opinions, however just remember Christians are supposed to welcome the sinners."
Twitter also saw a flood of comments yesterday with KingjohnkeyIII tweeting "I hear Lighthouse Church banned Anika Moa because they thought she was an actual Moa, back from extinction, thereby proving evolution."
"Anika Moa snubbed by church for being gay, Oh come on! 21st century people," Onie Wan Kenobi said.
Anika herself tweeted, "Just going to lesbian myself up and go for a lesbian walk. Maybe I should eat some lesbian apples? Oops I just lesbian farted."
The concert will go ahead in St Mark's Church, Carterton on March 23.
Reverend Jenny Chalmers said St Mark's was looking forward to hosting such a great musician and were not concerned about her sexuality.
"The Lighthouse Church people seem to have some views about her sexual orientation but they're not views that we hold in common. I think it's sad to hold judgmental views about anyone."