The investigation was launched after two GPs complained to the GMC about Dr Webberley’s private clinic, which specialises in gender issues.
She told the BBC she had given cross-sex hormone treatment to one 12-year-old and three 15-year-olds, despite NHS guidelines that they be given at about 16 or over.
“There are many children under 16 who are desperate to start what they would consider their natural puberty earlier than that,” Dr Webberley told BBC Wales.
“And, of course, when someone mentions a 12-year-old it is very emotive.”
She pointed out there had been “no decisions or judgements” made on the claims against her and they were “simply aspects that need to be explored”.
The restrictions imposed by the GMC on 7 May mean that all of Dr Webberley’s work with transgender patients will have to be supervised until November 2018.
She is unable to practise until she finds an approved clinical supervisor, which Dr Webberley says she is currently putting in place.
Stephanie Davis-Arai, of parents group, Transgender Trends, said she was “very concerned” by the move toward “earlier and earlier” treatment for “younger and younger” children.
“Teenagers [and children] are not really equipped to make long-term decisions and benefit and risk calculations. We should not be fixing their identity at that age with medication that is irreversible,” she added.
She said cross-sex hormone treatment can effectively put patients on the path to sterilisation, alongside other changes, which is a “huge ethical issue”.
“These are huge, life-changing effects on children’s bodies, on children’s lives, and we need to be very, very cautious before presenting this treatment pathway to minors,” she said.
Ms Davis-Arai called for “much-tighter regulation” for private GPs in this area.