The restaurants were initially told to close on August 21 after criticism from the Russian state food safety watchdog Rospotrebnadzor.
McDonald’s had been hoping to re-open its branches as soon as possible.
The company said it will appeal the rulings and is examining the judgements given by the court.
“We do not agree with the court’s resolution and will appeal against this resolution in accordance with the procedure established by law,” McDonalds said in a statement.
The company said it would do its best to continue its operations in Russia.
The Moscow restaurants affected are on Pushkin Square, Manezh Square, Prospect Mira and Varshavskoye Shosse.
Two regional McDonald’s outlets in Stavropol and Ekaterinburg also remain closed, following the allegations last week that the company had breached “numerous” sanitary laws.
“We will continue taking care of our employees and will do our best to continue the success of McDonald’s business in Russia,” McDonald’s said.
The court ruling comes amid a tense stand-off between Russia and the West over the situation in Ukraine.
The EU and US have imposed sanctions against Russia over its role in the conflict. Moscow has responded with a trade embargo against food imports from the West.
The safety watchdog, Rospotrebnadzor, has so far ordered the temporary closure of a total of six McDonald’s restaurants in Russia and has introduced unscheduled spot checks in the fast food company’s outlets across the country.
Rospotrebnadzor has denied that its actions are politically motivated.
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