Bruce Adamson said no process had been set out for assessing whether 16 or 17-year-olds had the "capacity" to make a self-declaration or understood its significance.
His submission to the latest consultation on reform of the Gender Recognition Act will be a blow to the government, as he previously suggested the age at which children can legally change gender could be as low as 12.
The Scottish Government proposes to lower the age at which someone can obtain a Gender Recognition Certificate (GRC), which legally alters their sex replacing their original birth certificate, from 18 to 16.
The move is part of wider controversial changes to the GRA including reducing from two years to three months the timescale a person is required to live as the opposite sex and removing the need of a medical diagnosis of dysphoria to allow self-identification as transgender.
Mr Adamson said the Scottish Government had not provided evidence to back a move to three months for under-18s.
He also said there was “no mechanism in the proposed reforms for setting out how an individual child's understanding of the process and its consequences would be assessed.
"The Scottish Government has not set out the way in which the process of statutory declaration would seek to balance these considerations for 16 and 17-year-olds, or indeed, for younger children who may be assessed as having the capacity and understanding to make this decision."
He said the government needed to do “more work” to address concerns "before bringing a Bill to the Scottish Parliament" and added: “We note in particular that there appears to be little research into the circumstances of children who choose to detransition, and therefore little on which to base decisions around the appropriate levels of protection and safeguards.”
His comments came after it was revealed that more than 50 16 and 17-year-old girls from Scotland been approved for mastectomies in order to change their gender.
A Scottish Government spokesman said: "We will take into account responses to the consultation, along with other evidence, ahead of introducing the Bill to parliament."