Under election rules a maximum of five per cent of the signatures can be declared invalid.
According to the CEC, in Kasyanov's case, 13.36 per cent were rejected.
Kasyanov served as prime minister under Putin from 2000-2004 but has since joined forces with the Kremlin leader's fiercest critics, such as Garry Kasparov, the former chess champion.
The March 2 presidential vote is all but sure to be won by Dmitry Medvedev, an ally of Putin, currently serving as deputy premier and head of Gazprom, the Russian gas company.
The other candidates are Communist Party leader Gennady Zyuganov and ultra-nationalist Vladimir Zhirinovsky, both polling at less than 10 per cent, and little-known politician Andrei Bogdanov. He is forecast to win less than one per cent. 'Joke'
Putin is barred from seeking re-election after serving two consecutive terms. He says he could become prime minister if Medvedev takes over the presidency.
This appears to be a certainty given the lack of open debate and the massive push by the Russian state media to promote Medvedev.
Ever since Medvedev's registration on January 21, he has been a constant presence on state news broadcasts, even accompanying Putin on an official trip to Bulgaria, as well as a high-profile hospital opening in a Russian province.
Zyuganov says he is considering withdrawing from a contest that risks becoming a "joke".