A new gender self-identification law passed by Scotland on Thursday may be blocked by Westminster.

The Gender Recognition Reform (Scotland) Bill was passed by MSPs by 86 votes to 39 on Thursday, paving the way for 16 and 17 year olds to change their legal gender. 

The change to the law will also reduce the waiting period from two years to just three months - or six months for 16 and 17 year olds - and remove the need for a medical diagnosis of gender dysphoria. 

Supporters hailed it a historic day for equality in Scotland but feminists have decried the assault on the rights of women and girls, and Christians fear for religious liberty.

After the Bill was passed on Thursday, Kemi Badenoch, UK Minister for Women and Equalities, said that the Scottish government had "not addressed the full implications of their bill – especially on the lives of women and girls".

She expressed disappointment that "sensible" amendments had been voted down and added, "The UK government is now looking at provisions that can prompt reconsideration and allow MSPs to address these issues."

Scottish secretary, Alister Jack, has said: "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."

A Scottish government spokesperson told the Guardian that it will "vigorously" contest any challenge by Westminster.

"The bill as passed is within legislative competence, and was backed by an overwhelming majority, with support from all parties," they said.

"Any attempt by the UK government to undermine the democratic will of the Scottish parliament will be vigorously contested by the Scottish government."

Lamenting the passing of the Bill, The Christian Institute's Scotland Officer Nigel Kenny said it was "a very sad reflection of the current closed-mindedness of most Scottish politicians". 

"Despite the fact that two thirds of Scots do not want this legislation, despite all the concerns from women's rights groups, the Equality and Human Rights Commission and the United Nations, the majority of MSPs chose to ignore women's and teenage girls' safety and ploughed on regardless with what former Labour leader Johann Lamont has rightly described as 'one of the most dangerous and misguided Bills in Holyrood's history'," he said.

"It seems likely now that, one way or another, this legislation will end up before the Supreme Court. It's proving to be a depressingly regular thing."

Earlier this week, Catholic bishops in Scotland expressed "grave concerns" over the Bill and warned that removing the need for a medical diagnosis of gender dysphoria would reduce "the opportunity for crucial healthcare, support, and protection for vulnerable individuals, including children".

"Children must be protected from making permanent legal declarations about their gender which may lead to irreversible elective interventions, including surgery"," they said.

"Lowering the minimum age from 18 to 16 and introducing a system of self-identification will put more children and young people on this path.

"Our concerns are amplified by the intervention of the Scottish Council on Human Bioethics, which has described the Bill as 'unsafe' and likely to harm young people."

They added, "The freedom to hold the reasonable view that sex and gender are given and immutable and disagree with the idea of gender as fluid and separable from biological sex should be upheld, particularly for those who work in education, healthcare, the prison service, or as marriage celebrants who, from both reasonable and religious perspectives, hold an understanding of marriage as a union between one man and one woman."