Alister Jack claimed he shared “the concerns” some had over elements of the measures, and promised ministers would look at the bill very closely.
His comments came after the bill finally passed 86 to 39 in favour, with Scottish Labour and the Scottish Liberal Democrats backing the bill alongside the majority of SNP/Green MSPs.Mr Jack 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.”
Scottish Conservative shadow equalities spokesperson Rachael Hamilton MSP also criticised the bill, claiming it puts women’s safety at risk.
She said: “The majority of Scots – let alone the women’s groups who campaigned vociferously against it – will be dismayed that this flawed and potentially dangerous bill has been passed by a majority of SNP and Labour MSPs.
“We all support improving the experience for trans people but that should never come at the expense of the safety of women and girls, and their hard-won rights.
“For a majority of MSPs to vote against an amendment that would have prevented convicted sex offenders from applying for a Gender Recognition Certificate will astonish and outrage most Scots.
“The fact that no substantive amendments to the legislation were passed demonstrates how impervious many MSPs – particularly from the SNP and Greens – were to reasoned argument and public opinion on this divisive issue.”
The changes will also drop the minimum age for applying for such a certificate from 18 to 16, and bring down the time a person is required to live in their acquired gender.
Protests briefly interrupted proceedings as Social Justice Secretary Shona Robison brought the debate to a close, with both applause and shouts of “shame on you” from the public gallery.