Sir Keir Starmer has said 16 is too young for people to self-certify their gender without going through medical checks.
The Labour leader said the idea gave him "concerns", despite his own party voting for such a change in the Scottish Parliament last month.
Supporters of the controversial Gender Recognition Reform (Scotland) Bill say it improves a lengthy and invasive process faced by trans people and that it could help society accept them for who they are.
Opponents say it opens up the possibility of predatory men to exploit the system, putting women in single-sex spaces at risk.
As well as lowering the minimum age to change gender, and removing the need for a gender dysphoria diagnosis, the law also drops the time required for an applicant to live in their acquired gender from two years to three months.
This rises to six months for those aged 16 and 17 with a three-month reflection period.
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Speaking on the BBC's Sunday With Laura Kuenssberg show, Starmer said that while Scottish Labour backed the reform, it doesn't represent the party's stance on a national level.
But he didn't have a clear plan of action for a Labour government in Westminster, saying: "We want to modernise the system, we're looking at what the options are, there are all sorts of different definitions in relation to self-certification."
Opponents have said the legislation could clash with the Equality Act, which allows the provision of separate or single-sex services and spaces.
Starmer said: "I have concerns about the provision in Scotland, in particular the age reduction to 16, in particular the rejection of our amendment in relation to the Equality Act."
When pressed on whether he thought people are old enough at 16 to get a gender recognition certificate based on self-identification, he said: "No, I don't think you are."
Asked if he thought this meant his party was wrong to back the SNP's bill, Starmer said: "That was a matter for Scottish Labour. I'm telling you what the position is in relation to the whole Labour Party."
Starmer added that safe spaces for women are "important" and something he "fundamentally believes in", but that he wanted to see "respectful debate" on the issue.
"At the moment this is treated as a political football from start to finish," he added.
Rishi Sunak's government is believed to be preparing to block the bill, and Starmer said he would wait and see what it says before deciding whether Labour should offer its support.
Also appearing on the show was transport secretary Mark Harper, who told Kuenssberg: "One of the things we are waiting to see is some detailed legal advice on the impact of such a piece of legislation on the rest of the United Kingdom."
He said: "There are conflicting rights here, there are trans people who have suffered discrimination and want their rights respected, but equally I've listened very carefully to the concerns that many women have had about risks to their safety."
Pointing to how heated the debate on this issue often becomes, Harper referred to how author JK Rowling said some "very reasonable things that people are entitled to say" on trans rights, and has been "treated very badly in response".
He added: "I think [with] this discussion it's best if we talk about it thoughtfully and carefully, which is why the government is not rushing to a conclusion but is waiting to see that detailed legal advice."