More than 300 people were inside the Pulse nightclub in Orlando when the sound of gunfire began to rip through the air just after 2am.
The killer moved into the nightclub, firing repeatedly, before taking dozens of revellers hostage.
Revd Peter Ould said it was an "absolutely atrocious crime" that was homophobic "in the truest sense of the word".
He added: "The fact that this was a gay nightclub was not incidental it was deliberately chosen by the murderer to go in and kill as many gay people as possible.
"There are lots of implications for Christians on how to respond to that. Some of the responses that I've seen online in the last 24 hours have been great. Some have been woefully inadequate."
Doctors fear the death toll from the deadliest mass shooting in US history will rise, as the identities of the 50 people who were gunned down began to emerge.
So far 15 victims aged between 20 and 50 have been publicly identified as victims of Omar Mateen, 29, who massacred revellers and at least one employee at a gay nightclub in Orlando, Florida.
According to reports the bodybuilder, who was of Afghan origin, telephoned police and pledged allegiance to Islamic State before he opened fire on the crowds with an assault rifle and handgun.
The terror group has since claimed responsibility for the attack, which was described by President Barack Obama as an "act of hate".
Revd Peter Ould continued: "This is a very physical expression of the naked hatred that some people in this world have for gay people.
"So praying for my gay and lesbian friends here because actually this is a moment where you go, yes there are still people here who hate us."
Revd Peter Ould speaking to Premier's Aaron James: