The UK Government could move to block legislation aimed at reforming how a gender recognition certificate can be obtained.
Alister Jack said Westminster may seek a section 35 order to prevent the Gender Recognition Reform (Scotland) Bill receiving Royal Assent after the laws passed a vote at Holyrood on Thursday.
MSPs voted 86 to 39 in favour of the controversial legislation after working through more than 150 amendments in two marathon sessions earlier this week.
Campaign groups had warned that the reforms – which seek to make the process for people to obtain a gender recognition certificate easier – could risk the safety of women and girls.
Supporters of the changes insist that it is about simplifying the process and removing hurdles within the current requirements.
But the process could be blocked if the Scottish Government’s Westminster equivalents exercise their powers to prevent the laws “having “an adverse effect on the operation of the law as it applies to reserved matters”.
The secretary of state for Scotland, said the “ramifications” of the legislation for UK laws would have to be explored and did not rule out an order stopping the Bill from receiving Royal Assent.
He added: “We share the concerns that many people have regarding certain aspects of this Bill, and in particular the safety issues for women and children.
“We will look closely at that, and also the ramifications for the 2010 Equality Act and other UK wide legislation, in the coming weeks – up to and including a Section 35 order stopping the Bill going for Royal Assent if necessary.”
The UK equalities minister, Kemi Badenoch, previously raised concerns the bill passing could create a “divergence” between laws in Scotland and England.
Under the reforms, the age limit for applications for a gender recognition certificate will be lowered from 18 to 16.
A requirement for a medial report, including a diagnosis of gender diagnosis, will be dropped.
Applicants for a certificate will also now be required to live in their acquired gender for three months – six months for 16 and 17-year-olds – down from the current requirement of two years.
An amendment submitted by SNP MSP Gillian Martin to ensure that anyone subject to a sexual harm prevention order, or a sexual offences prevention order, cannot seek a gender recognition certificate, is also being implemented having been accepted by MSPs.
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