The NWJCC said in some cases patients did not meet “the basic requirements for surgery”.
Having an unsuitable body mass index (BMI) – a value derived from an adult’s height and weight, was a factor.
There were also worries about whether wider health needs had been fully considered.
Some clinical professionals, it said, had concerns about whether parts of the referral assessment process had been done appropriately.
The NWJCC said it would commission an independent review of the service, and was “working with experienced gender specialists to start the review as quickly as possible”.
Health minister Mabon ap Gwynfor and deputy first minister Sioned Williams attended the meeting with the NWJCC.
After the Welsh government said: “Ministers sought and received assurances that the decision is a pause, not a stop.
“Each relevant case will be reviewed, and once the JCC has assurances that appropriate clinical assessments are in place, individuals will progress to surgery at the earliest possible opportunity.”
The decision to pause surgeries last week was prompted by data which indicated “significantly higher rates of referral for gender affirming surgery… compared with English gender services” in 2025-26, according to the health board.
First Minister Rhun ap Iorwerth previously said the review into surgery services must be quick.
Ap Iorwerth said while the committee at the heart of the row had taken the decision “for the right reason” on service quality grounds, he wanted a “resolution quickly”.