* Sahrawi's Polisario cheers court backing on deals
* Morocco sees no effect on deals covering Sahara region
* Tensions in disputed region high over military standoff (Adds Morocco reaction, Western Sahara context)
By Michele Sinner
LUXEMBOURG, Dec 21 (Reuters) - Two political and trade deals between Morocco and the European Union do not apply to Western Sahara, the European Court of Justice said on Wednesday, in a ruling that a group seeking the disputed territory's independence said was a victory.
The court said the two pacts from 2000 and 2012 aimed at closer trade and political ties were valid but could not include Western Sahara because the treaties did not specifically refer to it.
In the most significant ruling on the territory in years, the court said that for the purposes of the EU agreements, the term "territory of the Kingdom of Morocco" did not encompass Western Sahara.
Morocco claims sovereignty over the sparsely populated stretch of desert to its south, which has offshore fishing as well as phosphate and possibly oil reserves.
The Polisario Front independence movement, which says that Morocco illegally annexed Western Sahara in 1975, said the ruling showed that "Western Sahara is not part of Morocco".
"The ruling confirms the long-established legal status of Western Sahara as a non-self-governing territory," Polisario's envoy to Europe, Mohamed Sidat, said in a statement.
The court ruling appeared to sidestep a related diplomatic standoff with Morocco by overriding an earlier decision by the lower General Court that the EU trade deals were void. At the time, Morocco briefly suspended contact with EU institutions and the EU to lodge a legal appeal.
Morocco's foreign ministry praised the overiding of the earlier ruling and said the court had not called into question the "legality and legitimacy of Morocco's international deals" covering the Moroccan Sahara region, the term the kingdom uses for the Western Sahara.
Without going into details of the trade deals, the ruling signalled that some EU fisheries in disputed coastal waters would be in violation of the ruling, as the court said agreements signed with Morocco could not include Western Saharan resources, given that its inhabitants had not agreed to that.
"It does not appear that this people has consented to the agreement being applied to Western Sahara," the court said.
The EU and Morocco have struck agreements allowing duty-free quotas for agricultural products such as tomatoes and granting access for European vessels to fish in Moroccan waters in return for financial assistance. The two sides also began negotiations in 2013 to form a deeper and broader free trade agreement.
Western Sahara has been contested since 1975 when Spanish colonial powers left. Morocco claimed the territory as it own and fought the 16-year war with Polisario which established its self-declared Sahrawi Arab Democratic Republic. (Additional reporting by Aziz El Yaakoubi in Rabat; Writing by Robin Emmott in Brussels; Editing by Andrew Heavens and Patrick Markey)