A spokeswoman for the commission said that "there will be a second count of the signatures and the final decision will be taken in a CEC meeting... by Sunday".
Speaking in Brussels, where he was attending a conference with liberal European parliament members, Kasyanov called the allegations "simple propaganda".
He said he still expected to be included on the ballot when the CEC makes its decision.
Kasyanov said: "There is no decision of central commission, the decision is planned for Saturday and that's why there is a dialogue between my technical people and people from the central commission.
"We insist that this is simple propaganda that the signatures are not real. Only 200 signatures out of 600,000 signatures are put on doubt. Only 200, only 200, 0.005 percent only. All others are technical adjustments.
"That's why we insist that the quality of all signatures is the best, of high level. That's why there is no reason not to register, and I expect Saturday a decision for registration."
Yelena Dikun, Kasyanov's spokeswoman, said that "lawyers from the campaign team are working on this now and will take our complaint to the CEC".
Dmitry Medvedev, Putin's hand-picked successor, is the overwhelming favourite to win the election.
Glowing reports on state television on Thursday showed him touring an aircraft factory and a military barracks.
Kasyanov, who represents Russia's small and increasingly beleaguered anti-Kremlin opposition, has called the forthcoming election "dishonest and unfair".
The requirement to gather two million signatures is a big hurdle for independent candidates.
Under electoral laws, a candidate can be registered if no more than five per cent of the signatures are judged invalid, far below the 13.38 per cent of spoiled signatures allegedly on Kasyanov's list.
Meanwhile. Andrei Bogdanov, a little-known politician, has become the fourth candidate to successfully register for the March 2 election to replace Vladimir Putin.
Bogdanov's achievement in collecting two million signatures was all the more remarkable given the lack of coverage of independent candidates in the state-dominated media.
His almost unknown Russian Democratic Party won just 0.13 per cent of the vote in December parliamentary elections, or a total of 89,780 votes.
The other candidates registered are Gennady Zyuganov, the Communist party leader, and Vladimir Zhirinovsky, the ultranationalist politician, both of whom are forecast in opinion polls to win less than 10 per cent each.