He said the party expected to appeal the ruling by the Zamoskvoretsky District Court and eventually bring it to the European Court of Human Rights.
The party held its first founding congress in December 2012, and in May the ministry rejected its application to be registered. As a result, the party had to hold a founding congress for the second time in June, but in July its request for registration was rejected again.
On Sunday, the People's Alliance held yet another founding congress, at which Navalny formally joined the party and was elected its leader, and is launching its third attempt to be registered.
Critics have argued that the Justice Ministry has routinely refused to register opposition parties and that only one registered party, RPR-Parnas, has no links to the Kremlin.