* Rabat bars ministries from talking to EU delegation-document

* Government still in contact at high level with EU

* Move follows EU court's decision to annul trade deal

* Disputed Western Sahara region at centre of row

By Aziz El Yaakoubi

RABAT, Jan 28 (Reuters) - Morocco has suspended contacts with the European Union delegation in Rabat over a trade row, a confidential Moroccan government document showed, a move that could slow multi-million dollar development projects.

The dispute has arisen at a sensitive time as the North African kingdom has played a growing role in security cooperation, helping France and Belgium track Islamist jihadists who carried out last year's Paris attacks.

But Rabat's decision stopped short of a formal suspension of ties, and an EU source said the government remained in regular contact with high level EU officials, including foreign policy chief Federica Mogherini.

Two other EU sources said the suspension may disrupt around 1.03 billion euros ($1.12 billion) of funding that the European Union has granted to the North African kingdom.

"To keep projects working and funds flowing, meetings and information exchanges are needed. That is how the money is disbursed," one EU source said.

The Moroccan foreign ministry asked government departments to suspend contacts and not to arrange meetings with the EU team in Rabat, the document showed, after an EU court last month cancelled a trade agreement with the kingdom, saying it should not include the disputed West Sahara region.

The EU funding program includes some 188 million euros to support Morocco's advanced status with Brussels, 125 million euros for education, 100 million euros in health support and some 75 million euros to reform the judiciary in the country.

Other funds were expected to be signed in 2016.

Several European traders said the dispute appeared to have delayed the opening of Morocco's EU wheat tariff import quota -- an agreement with the EU under which Morocco opens tenders for imports. It was not possible to confirm whether the row was to blame.

"This unusual delay looks like a political imbroglio at a time when imports have started late and there is a drought threatening the next harvest," one trader said.

An EU source, who declined to be named due to the political sensitivity of the issue, said the delegation had received no official communication from the government regarding a hiatus, but confirmed there had been no meetings for several weeks.

The Moroccan government spokesman and foreign ministry were not immediately available to comment but the country's ambassador to the European Union, Menouar Alem, told state news agency MAP relations with the bloc were currently on a "break".

"There is no cut in diplomatic ties between Morocco and the EU... However, we are in a situation of a break until Morocco has some visibility on the legal security of the relationship that it has with the E.U.," ambassador Alem said.

A EU delegation spokesperson declined to comment.

SAHARA DISPUTE

In Brussels, an EU spokesperson also declined to comment on the document, but an EU source said a high level EU official had visited Morocco last week to discuss "all issues related to our cooperation".

The source added: "The EU's foreign policy chief Federica Mogherini is in regular contact with the Foreign Affairs Minister to whom she talked yesterday."

The reported contacts made it appear unlikely there would be any impact on Rabat's security cooperation and intelligence-sharing with France and other European states.

The kingdom provided the tip-off that allowed French police to locate Paris attacker Abdelhamid Abaaoud, has held Abaaoud's brother Yassine since October and issued an arrest warrant for Salah Abdeslam, who is suspected of taking part in the attacks.

The Moroccan king agreed with German Chancellor Angela Merkel in a telephone conversation on Wednesday about repatriating illegal migrants to Morocco, a move that will help Germany limit migration from North African countries.

Morocco has controlled most of Western Sahara since 1975 and claims the sparsely populated stretch of desert, which has offshore fishing, phosphate reserves and oilfield potential, as its own.

Morocco's annexation of Western Sahara prompted a rebellion by the opposition Polisario Front, which has been backed by Morocco's neighbour Algeria. The United Nations brokered a ceasefire in 1991, but talks have since failed to find a settlement in Africa's longest-running territorial dispute.

A legal case was brought to the court by the Polisario front and involves trade of agricultural products, processed agricultural products and fisheries. The court decision was announced on Dec. 10 ruling in favour of Polisario.

EU institutions said after the court decision that they would appeal the ruling, but a second decision from the European court will take months or even more, sources said.

Rights groups such as Amnesty International and Human Rights Watch accuse Morocco of continuing to use excessive force against activists and repressing political freedom in Western Sahara. Rabat invests heavily there, hoping to calm social unrest and independence claims.

Any investment involving international firms and foreign governments stirs controversy over the legitimacy of Moroccans to negotiate on behalf of the Western Saharan population.

EU lawmakers approved a fisheries agreement with Morocco in 2013, allowing European ships into Moroccan and Western Saharan waters, two years after rejecting a similar deal out of concern it might not benefit the local population.

(Additional reporting by Robin Emmott in Brussels and Valerie Parent in Paris; editing by Patrick Markey and Philippa Fletcher) ((aziz.elyaakoubi@thomsonreuters.com; +212623934595)(;))

Keywords: MOROCCO EU/WESTERNSAHARA