The ministry said on Thursday it was looking into the allegations that more than 93 million rubles (S$3.67 million) of state funds had been stolen. It didn't identify possible culprits.
Russian news reports said that police were searching the offices of the Ministry of Regional Development in Moscow and its branch in the Pacific port of Vladivostok as part of the investigation.
Russia had allocated US$20 billion for hosting September's APEC summit in the long-neglected city. Critics have said too much was spent to impress the visitors, especially given the area's more acute needs, and some reports have alleged that part of the money was stolen.