An opposition bloc that includes Kasyanov's 'People for Democracy and Justice' said it would take the case to the European Court of Human Rights.
Kasyanov's website said that despite minor violations, the party's registration was fully in line with the law, with party offices established in 54 regions of the country, and the number of members exceeding 56,000 people.
"The Federal Registration Service's claims cite reports of 37 party members breaking the law, which in no way affects the legality or legitimacy of party's establishment as a whole," the website said.
The party's founding congress was held in September 2007 in the Moscow Region. The registration service refused to register Kasyanov's party in January 2008, citing violations of laws on political parties. In particular, party member lists submitted to the service reportedly contained underage or dead persons.
Earlier, representatives of Kasyanov's party had questioned the registration authorities' right to continue their role as defendant in the case, given that the service's functions are being transferred to the Justice Ministry.
However, a spokesman for the service said on Tuesday that it would continue to be the defendant for the time being, as the Justice Ministry will not take over until October.
Konstantin Merzlikin, presidium secretary of the Russian People's Democratic Union bloc, which includes Kasyanov's party, told reporters on Tuesday that the case would be taken to the Strasbourg court later this month.
"In the coming month, we will collect documents and file a complaint to the European Court. The service's decision was political, just like today's Moscow City Court ruling," he said.
Judges have told party representatives that the party is entitled to resubmit documents for registration if it rectifies all violations.