In a statement to MAP state news agency, the agriculture ministry said the EU should resist any attempts to block Moroccan products entering into the European market but did not explain why the pact might be at risk.

"In the absence of a frank commitment from the European Union, Morocco will have to make a decisive choice whether to continue with EU trade or to undo it without looking back, and focus on building new trade routes," the ministry said.

The European Court of Justice ruled in December that deals involving trade of agricultural products, processed agricultural products and fisheries between the EU and Morocco did not apply to Western Sahara.

The ruling was claimed as a victory by the Polisario group seeking independence for Western Sahara, which Morocco calls its own. Last month, Polisario sought to have the EU apply the ruling to block a shipment of fish oil to a French port from the territory.

Rabat had said the European court ruling would not impact current trade deals in any way. The agriculture ministry said on Monday that current agreements with EU ensured thousands of jobs and could trigger migrant flows if their implementation fails.

An EU diplomatic source told Reuters the ministrys statement came after Energy Commissioner Miguel Arias Canete referred in a written reply to a question in the EU parliament to the "separate and distinct" status of Western Sahara.

Moroccan agriculture minister Aziz Akhannouch said Mondays statement was not a response to Canetes remarks, but that his comments reflected an attitude seen within EU institutions.

"It is about what the European court decision means," the minister told Reuters by telephone. "For Morocco it means the deals should be implemented like they have been since their signature."

Akhannouch said European officials have not yet started official talks on the meaning of the ruling but that Morocco has been preparing for its potential effects.

"We are reasonable people, we know that we need Europe and Europe needs us. But we want them to see all the efforts Morocco does to make the partnership work," he said.

Without going into details of the trade deals, the court had signalled some EU fisheries in disputed coastal waters would be in violation of the ruling. It said agreements signed with Morocco could not include Western Saharan resources because the regions inhabitants had not agreed to that.

Western Sahara, which has significant phosphate reserves and offshore fishing, has been contested since 1975 when Spain, the former colonial power, withdrew. Morocco fought a 16-year war with Polisario, which established a self-declared Sahrawi Arab Democratic Republic.

A 1991 ceasefire was meant to be followed by a U.N.-backed referendum on self-determination including the question of independence. The vote has never happened mainly because of disagreements on who could take part and Morocco since 2006 has promoted its own autonomy proposal.

The two sides often engage in diplomatic sparring but tensions on the ground have also increased since August last year, when UN peacekeepers were forced to deploy after Morocco forces and a Polisario unit faced off in a buffer zone between Morocco-controlled area and territory held by Polisario.

Last month, Morocco rejoined the African Union, having left decades ago because it had allowed Polisario recognition. Analysts expect Morocco to try use its position inside the AU to promote its own autonomy plan for Western Sahara against Polisario.