Ten Welsh Premier League clubs have been granted a domestic licence but The New Saints and Neath have had their applications rejected.
The Football Association of Wales Club Licensing First Instance Body assessed 21 applications.
A domestic licence, which was introduced in 2010, is required for every club to maintain their status.
The New Saints and Neath will have the chance to appeal before an independent panel later this month.
Along with the 10 other Welsh Premier sides, three clubs from the two feeder leagues have also been awarded a licence.
They are GAP Connah's Quay and Llandudno from the north Wales-based Cymru Alliance, and Haverfordwest County from the Welsh League in the south.
The Saints currently lead the WPL by five points from Bangor City, with Neath,
who have suffered recent financial porblems,