The opposition viewed the regional campaign ahead of the September vote as a dress rehearsal for next year's parliamentary election.
The three men say they will continue their protest until the Central Election Commission reviews their case.
Volkov contested the commission's decision which found faults with over 1,300 signatures of the more than 11,600 they submitted, saying that the main argument behind the refusal was the commission's reference to an outdated ID database.
"If they were considering our filing in a purely legal way, we would be using only legal methods, too," Volkov told The Associated Press on the phone from Novosibirsk. "One had to show that for some people, reputation and dignity are not just empty words - it was a spontaneous move triggered by the way (the decision) was taken."
Volkov said he was confident that a new check of the signatures would prove them right.
Opposition leader Alexei Navalny was canvassing in Novosibirsk and two other big cities earlier this summer in a bid to energize the voters and said Monday's decision of electoral authorities is an ominous sign before the 2016 Duma vote.
"These three brave and honest men have gone on hunger strike to protect electoral rights of all Russians," he wrote in his blog. "The way the opposition was thrown out from election ballots in Siberia is going to replicate tomorrow across the country, and this scenario will be used for the State Duma election as well."