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Labour leader Sir Keir Starmer believes 16-year-olds are too young to change their legally recognised gender.
The UK Labour leader voiced "concerns" about the Scottish government's reforms to the process, citing a potential impact on UK-wide equalities law.
However, he stopped short of backing a challenge to the Holyrood legislation, something UK ministers are considering.
The SNP's Westminster leader Stephen Flynn said any move to block the bill passed by MSPs would be "an outrage".
The Scottish government has said it will "vigorously" contest any challenge.
The Gender Recognition Reform (Scotland) Bill, passed by MSPs, removes the need for people to get a medical diagnosis of gender dysphoria before starting the change process.
It also drops the age limit to 16, and cuts the amount of time the process takes from two years to a matter of months.
Scottish Labour supported the reforms, and almost all of its MSPs voted for the finalised bill.
But Sir Keir told the BBC's Sunday with Laura Kuenssberg: "I have concerns about the provision in Scotland, in particular the age reduction to 16 and, in particular, the rejection of our amendment in relation to the Equalities Act."
Pressed on whether he thinks someone of 16 is old enough to decide to change their gender, he replied: "No, I don't think you are."
Scottish Labour had tabled an unsuccessful amendment that sought to clarify the application of UK-wide equality laws in areas such as safe spaces.
Sir Keir also told the programme a respectful debate was needed on the issue and said he believed it was currently being treated as a "political football".
Asked to clarify his position, the Labour leader replied: "Modernise the legislation to take out the indignities."
The UK government is considering challenging the legislation, with Prime Minister Rishi Sunak saying it is "entirely reasonable" for ministers to examine the potential legal impact of the bill on the rest of the UK.
Sir Keir would not be drawn on whether he would back a challenge, saying he wanted to wait and see what UK ministers decided to do.
The UK government is currently considering legal advice about whether to use its powers to block the bill from becoming law.
Prime Minister Rishi Sunak spoke during a visit to Scotland last week about the concerns he has over the changes it would enact.
Downing Street officials said on Saturday that the full legal advice to ministers had not yet been reviewed and no decisions had been made.
UK Transport Secretary Mark Harper was also asked about the gender self-identification laws being changed in Scotland.
He said ministers were awaiting "detailed analysis" of how Scotland's gender law would affect UK legislation.
Mr Harper told the BBC: "We are not proposing to make those changes for England, but what we have to do is make a decision about whether that legislation impacts on legislation elsewhere in the UK.
"One of those pieces of legislation is the Equalities Act.
"That is why we need a detailed analysis of that, and that is the information the government needs before it can take a decision."
'That's an outrage'
Mr Harper added that transgender people had received abuse and their rights should be respected but women also had concerns about risks to their safety.
The minister also described criticism of the author JK Rowling, who has condemned the legislation in Scotland, as unfair.
Meanwhile, SNP Westminster leader Stephen Flynn defended the reforms.
He told BBC Scotland's The Sunday Show: "What we have is a right-wing UK Conservative government which is seeking to row back on the democratic powers of the Scottish Parliament. That's an outrage.
"And the people who should be most outraged by that are the Conservative and Labour politicians who voted in favour of the GRR (Gender Recognition Reform) who must recognise the fact this is the UK parliament overstepping massively."
The Scottish Greens criticised the Labour leader and said his comments were a "shameful intervention".
Equalities spokeswoman Maggie Chapman said: "Starmer is ignoring the views of the vast majority of the Scottish Parliament, including the Labour MSPs who rightly backed the bill.
"A lot of people in Scotland will never forgive him if he lines up with the Tories to block what is a small but important step for equality."