The Court of Arbitration for Sport says Murofushi and the Japanese Olympic Committee are challenging the IOC's decision to annul his election as an athletes' representative during the London Games.
"The matter is of extreme importance to Murofushi, an athlete who is proud to have adhered to the Olympic values throughout his career," JOC official Yasuhiro Nakamori said Tuesday in a statement.
Murofushi won gold at the 2004 Athens Games and bronze at the London Olympics, where he was among 21 athlete candidates competing for four IOC member seats. Almost 7,000 athletes — a 64 per cent turnout — voted.
Though Murofushi and taekwondo fighter Chu Mu-yen of Taiwan finished in the top four places, the IOC board barred them from accepting their eight-year posts for breaking election rules.
"While the Japanese Olympic Committee and Koji Murofushi respect the IOC's ruling, we believe that a misinterpretation of Murofushi's actions caused the current circumstance," Nakamori said.
Both athletes were punished for using computers to lobby voters; Chu was warned for distributing sweets.
Chu also intends appealing, and CAS said it has informed Taiwan Olympic officials how to file a challenge. CAS said the parties will submit documents and "a hearing may take place."
A January verdict could settle the dispute about the time that Japanese officials begin international campaigning in support of Tokyo's bid to host the 2020 Summer Games. The other bid cities are Madrid and Istanbul. IOC members vote in September 2013.
The IOC has delayed filling the athlete member seats during the appeal process.
With Murofushi and Chu removed, the election was won by Danka Bartekova (Slovakia, shooting); James Tomkins (Australia, rowing); Kirsty Coventry (Zimbabwe, swimming) and Tony Estanguet (France, canoeing).
The IOC athletes' commission includes 12 Olympians elected to represent their peers among the 100-plus IOC members.