"Our appeal was turned down," said Magomed Yevloyev, the founder of the web site, which is one of the only information sources criticizing authorities in the mainly Muslim region bordering Chechnya and is known for its investigations into local corruption.
Yevloyev called the ruling "unlawful" and promised that the web site would keep operating despite the court's decision, which came into force right away. He said the web editors should be able to keep the site open on a technicality.
"Only the web site's editors can decide on it being shut down, but they were not involved in the trial, so they are not planning to abide by it," he said.
The web site's editors will now file their own court appeal, he said.
The web site is currently without an editor-in-chief after Roza Malsagova, who had run the site since last year, fled the country with her three teenage sons in July. She is applying for political asylum in France.
Prosecutors opened a criminal case against Ingushetiya.ru in July on charges of inciting ethnic hatred. Moscow's Kuntsevsky District Court ordered that the web site be closed in June.
Yevloyev has blamed "political pressure" for the court case and called the investigation "an attempt to silence the last independent voice in the republic."
He also has argued that the authorities have no right to shut down the web site because it is registered in the United States.
Ingushetiya.ru promoted and helped organize a January 2007 protest in Ingushetia in which demonstrators armed with Molotov cocktails clashed with police and burnt a pro-government newspaper office.
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