Afan Lido, Gap Connah's Quay and Port Talbot Town have been refused the FAW domestic licence and the Uefa licence for the 2014-15 season.
The clubs have the right to submit an appeal with any appeal being heard by Tuesday, 22 April.
The nine other current season Welsh Premier League clubs have been awarded an FAW domestic cicence and a Uefa licence.
Cefn Druids, Haverfordwest County and Llandudno Town from the Welsh Premier's feeder leagues were also awarded the FAW Domestic Licence for next season.
But Conwy Borough and Flint Town United were refused a domestic licence.
The domestic licence is a pre-requisite to participate in the Welsh Premier League for 2014-15 season and the Uefa licence is a pre-requisite to participate in Uefa club competitions.