The judge also shrugged off suggestions that insisting on a gender reassignment operation was akin to torture, and said it was a consented choice which had medical benefits.

Speaking outside court, a disappointed Tse said he was not surprised by the ruling and vowed to lodge an appeal.

“My fellow applicants and I had recognised from the beginning that it was likely to be a long journey,” Tse said.

While their adopted gender was fully recognised in Britain, the commissioner refused to amend their gender on their local ID cards. Two of them held British passports recognising them as male, while the other had a gender reassignment certificate issued by the British government.

The refusal by the local authority prompted the legal challenge.

In his 59-page judgment, which came almost four years after the first challenge was filed, Au considered the predicament of having transgender people adopting their assigned gender on their ID cards.

He noted that many government branches, from hospitals to social welfare departments, all relied on the information on the card to make gender-specific arrangements and decisions.

Ignorance, Chinese values, religious dogma: LGBT Hong Kong students’ plight

The judge also raised problems that could arise from someone who had not undergone a sex-change operation reversing his or her gender.

In a female-to-male case, the person could get pregnant as soon as he had stopped his hormone treatment. “Is he the mother [which she really is], or the father [which the ID card appears to suggest that he is]?” Au said.

He said unless society changed, the medical procedure remained the only objective criteria on which authorities could depend for certainty and consistency.

During the trial, the trio’s lawyers described the department’s decision as “out of proportion” and amounting to torture or inhuman treatment, when it insisted their clients had to undergo the surgery.

But Au disagreed, and said the choice was not forced upon them “under duress or undue compulsion”. Rather, it came with medical benefits, he said.

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He likened it to someone who suffered from a non-life threatening condition – but one which caused that person to be discriminated against.

If they eventually decided to eradicate that condition, he said: “It is a free and considered choice of the person.”

Expressing his understanding with the trio’s plight, Au said it had not been “easy to make a decision in these very difficult and sensitive cases”.

“Although at the end I have decided in favour of the commissioner, the court is conscious of the situations faced by transgender persons who have not completed sex reassignment surgery.”

The case came after the city’s Court of Final Appeal issued a landmark decision in 2013 that allowed a woman – who had a sex-change operation after being born a male – to marry her boyfriend. The ruling gave rise to the Interdepartmental Working Group on Gender Recognition.

Au said he was pleased to see the government had been engaging in consultation.

But on Friday, Tse said it was the lack of legislative progress which had prompted him to initiate the court action.

Erick Tsang Kwok-wai, the director of the Immigration Department, under which the commissioner of registration works, said he welcomed the court’s decision.

“Under our policy, anyone who has a medical document after surgery can come to us to have their data changed on an ID card,” he said.

A spokesman for Amnesty International called the court decision “a blow to the recognition of transgender people”.

“No one should be forced to undergo gender affirming surgery in order to have their gender legally recognised,” he said, urging the government to take action.