The two most senior Anglican clergy have called on Christians to "speak out in support of LGBTI people" and said it is an "absolute call" on Christian discipleship to support persecuted gay people around the world.
The statement in response to the Orlando shootings was released on Monday by the Archbishops of Canterbury and York and says Christians must "love without qualification".
The archbishops said: "The obligation to object to these acts of persecution, and to support those LGBTI people who are wickedly and cruelly killed and wounded, bereaved and traumatised, whether in Orlando or elsewhere, is an absolute call on our Christian discipleship.
"It arises from the unshakeable certainty of the gracious love of God for every human being."
The intervention came after the Church of England was criticised because at first it did not acknowledge the victims of the Orlando shooting were gay in a prayer released immediately after the attack.
The Church tweeted a "prayer for Orlando" in the aftermath of the tragedy, which left more than 50 dead after a gunman rampaged through a gay nightclub in Florida. However the Church was attacked for its broad-brush wording.
Jayne Ozanne, an LGBT activist and member of the Church's general synod, called on it to "show a lead" in the response.
"I think it is very telling the way the Church has responded," she told Christian Today before the archbishops' statement was released.
"We have to recognise these are all God's children. Independent of what we think and our theology our first response as Christians has to be to come alongside and pray specifically for those affected."
Ozanne called on the Archbishop of Canterbury's official residence in London to fly its flag at half mast in response to the attack. "I think it would symbolise solidarity with all those affected and all those who feel a deep revulsion at what has happened," she said.
A spokesman for Lambeth Palace told Christian Today the Palace follows government guidelines for flying flags at half mast on public buildings and was "currently awaiting guidance".
Richard Cattley, a retired CofE vicar, accused the Church of "not wanting to address the issue and recognise it was an attack on the LGBT community. "It is as if we're saying 'it is awful' but not actually admitting what is happening here," he told Christian Today before the archbishops' statement. Others criticised the Church's prayer on social media.
The prayers used by the Church for tragedies are chosen from the CoE's website under a section of "prayers for peace and all those affected by violence". The same three prayers have been recylced for a number of events over the past two years including the Charlie Hebdo attacks, the Ferguson shootings, the Paris attacks, the Pakistan bombings and more. However a number of hours after the Church's first official prayer, the @c_of_e twitter account tweeted an alternative prayer written by Rachel Mann, a transgender Anglican vicar, who called for "furious solidarity with queer people". Mann prayed the Church would be "joyous in our celebration of your Rainbow People".
Arun Arora, the CoE's director of communications, told Christian Today: "Our prayers of lament focus on those who have lost their lives and their loved ones. All three of the prayers we have tweeted over the past 24 hours reflect that focus."
You can see the Church's full prayer below.