Speaking during a visit to a hospital in Welwyn Garden City, Mr Johnson claimed he was “sad” at the reaction of groups which pulled out of a UK-hosted global conference in protest, which has since been cancelled.
He said: “We will have a ban on gay conversion therapy, which to me is utterly abhorrent.
“But there are complexities and sensitivities when you move from the area of sexuality to the question of gender. There, I’m afraid, there are things that I think still need to be worked out.
“I’m sorry we haven’t been able to reach agreement with the organisations concerned but that will in no way diminish our determination to tackle prejudice wherever we can.”
Mr Johnson also said that he does not believe children should be able to take decisions about their gender or irreversible treatments without some parental involvement.
He explained: “I don’t think that it’s reasonable for kids to be deemed so-called Gillick-competent to take decisions about their gender or irreversible treatments that they may have. I think there should be parental involvement at the very least.”
Mr Johnson also said that he did not believe “biological males” should be competing in women’s sports and that women should have spaces in hospitals, prisons and changing rooms which were “dedicated to women”.
It came as Sir Keir Starmer called for ministers to honour their promises to ban all forms of conversion therapy.
Speaking during a visit to Bacup in Lancashire, the Labour leader said: “Conversion therapy in all its forms should be banned. That used to be the Government’s position.
“They have been flip-flopping on this over the last few days. The need to stick to their promises.”
Sir Keir accused ministers of using the issue to try to distract from the cost-of-living crisis as the rise in national insurance contributions kicked in.
“They know that what is keeping people awake at night is the cost of living, whether they can pay their bills or not,” he said.
“In order to try to distract from that the Government wants to create an argument about conversion therapy. It is not going to wash.”
Earlier on Thursday a former LGBT Government adviser has urged leaders to stop making “pathetic excuses”.
Jayne Ozanne explained conversion therapy and good medical practice, where people have a safe space to explore who they are without judgment, are two very different things.
She said: “Conversion therapy is about being told that you can never be trans, that there is an ideology at heart which stops someone being who they are.
“Of course these issues are complex, but that is why other international countries have found a way through.
“We’ve been working on this for four years. And it’s time that we stopped making excuses and got on with what our legal experts have told us is something relatively simple to do.”
Ms Ozanne quit her role as a Government LGBT adviser in March 2021, accusing ministers of creating a “hostile environment” for LGBT people.