A transgender man from Kent who gave birth with the help of fertility treatment cannot be registered as his child’s father, the most senior family judge in England and Wales has ruled.

In the first legal definition of a mother in English common law, Sir Andrew McFarlane, the president of the high court’s family division, ruled on Wednesday that motherhood was about being pregnant and giving birth regardless of whether the person who does so was considered a man or a woman in law.

Freddy McConnell, 32, who has lived as a man for several years but retained his female reproductive system and gave birth in 2018, went to court after a registrar insisted he was recorded as the baby’s mother on the birth certificate despite holding a gender recognition certificate that made it clear the law considered him male.

The ruling was quickly attacked by campaigners and lawyers as a blow to the rights of trans parents and their children and sparked calls, including from the judge, for legislative reform.

“Being a ‘mother’ or a ‘father’ with respect to the conception, pregnancy and birth of a child is not necessarily gender specific,” McFarlane concluded after McConnell requested a judicial review.

“There is a material difference between a person’s gender and their status as a parent. Being a ‘mother’, whilst hitherto always associated with being female, is the status afforded to a person who undergoes the physical and biological process of carrying a pregnancy and giving birth.

“It is now medically and legally possible for an individual, whose gender is recognised in law as male, to become pregnant and give birth to their child. Whilst that person’s gender is ‘male’, their parental status, which derives from their biological role in giving birth, is that of ‘mother’.”

McConnell, a Guardian multimedia journalist who had experienced gender dysphoria since childhood and realised he was trans in 2010, aged 23, said he was “saddened” by the decision in favour of the government and the registrar, which resisted McConnell’s claim to be recognised as his child’s father. He is considering an appeal.

“If it is upholding the status quo then I am really worried about what that this means not just for me but other trans people who are parents or who want to become parents,” he said.

“It has serious implications for non-traditional family structures. It upholds the view that only the most traditional forms of family are properly recognised or treated equally. It’s just not fair.”

McConnell has long lived as a male, starting testosterone treatment in April 2013 and undergoing chest reshaping surgery in Florida. In 2016, he sought advice from a fertility clinic about becoming pregnant. His hormone treatment was suspended, which had the effect of reversing some of the gender-reassignment process, leaving him destabilised, which he described as a “loss of myself”. His menstrual cycle restarted and he became pregnant in 2017 using sperm from a donor. He gave birth in 2018.

McConnell’s journey to parenthood was captured in a recent feature-length documentary, Seahorse, a reference to the fish that reproduce through male pregnancies.

Stonewall, the LGBT charity, said the ruling was “deeply disappointing” and failed to recognise trans parents for who they were. “It’s another example of how current legislation contradicts the fragile equality trans people currently have,” said Laura Russell, the director of campaigns.

Michael Wells-Greco, a partner at the law firm Charles Russell Speechlys, said the ruling “flies in the face of the social reality of this family” while the law firm Irwin Mitchell said it was time England “respect the human rights of the trans community” and follow Canada and Sweden, which allow gender neutral birth certificates.

The judge praised McConnell for “properly and bravely” bringing his case and said there was a “pressing need” for the government and parliament “to address square-on the question of the status of a trans male who has become pregnant and given birth to a child”.

He said existing legislation and UK and European human rights case law “do not themselves directly engage with the central question”.

He conceded that “the social and psychological reality” of McConnell’s relationship with his child was as a father and this was in tension with the law as it stands.

In the Netherlands, for example, trans men who give birth are registered as fathers.

In July, McConnell’s anonymity in the case was lifted following applications from news media organisations who argued the self-generated publicity around the pregnancy and birth in the film and the public interest in the question of how the state recognised parenthood meant his identity should be known.

McConnell’s wish to be registered as his child’s father plunged him into a web of different laws. His intrauterine insemination fertility treatment was governed by the Human Fertilisation and Embryology Act 2008 which defines treatments as “assisting women to carry children”, his gender reassignment was under the Gender Recognition Act 2004 and he registered the birth under the Births and Deaths Registration Act 1953 which allows for people to tick “father/parent” only where a woman is to be a second female parent .

The registrar’s insistence McConnell be registered as “mother” appeared to him to be a result of an administrative need for every child to have a registered mother and was a breach of McConnell’s rights under the Human Rights Act 1998, his lawyers argued. Finally, those acting for the child applied under the Family Law Act 1986 for a declaration that McConnell was his father.

A representative for the child told the court that it was important for his identity and self-esteem that the birth certificate “reflects the reality of his life”.

“Father means male parent,” they said. “That is exactly what [McConnell] is. Anything else gives the impression of something secretive or shameful. This could lead [the child] to feeling excluded for society and that he is different or odd.”

McFarlane concluded the decision to register McConnell as a mother did not breach his or his child’s human rights and, given the Gender Recognition Act was both retrospective and prospective, it was also in line with that law.

The Aire Centre, a legal charity that helps people assert their human rights, also intervened in the case to highlight the right of children to be protected from discrimination due to the sexual orientation or gender identity of their parents, as well as children’s right to know their lineage.