It has given permission for a judicial review to go ahead after examining Guernsey's case.
In July, the UK Department for Environment, Food and Rural Affairs and the Marine Management Organisation announced that it was suspending the agreement.
It stemmed from a disagreement over its interpretation, with the UK wanting Guernsey to implement quotas on the Bailiwick fleet fishing in Bailiwick waters.
At the same time, Defra and the MMO suspended the UK licences held by skippers of some Bailiwick vessels.
It meant that 28 locally-registered boats under 10m were prevented from fishing in UK waters.
It also meant that Bailiwick fishermen could not work in EU seas.
Defra confirmed at the time that a total of 17 UK boats – 13 over 10m. long and four below 10m. – were licensed to fish in Guernsey waters.
