"A repeat of the run-off vote may fail to work," Putin told outgoing Ukrainian President Leonid Kuchma on Thursday at a meeting at an airport outside Moscow.
"The re-run can be held twice, three times, 25 times until one of the parties gets the desired result," Putin said.
Kuchma arrived in Moscow to consult Putin on the political crisis sparked by the disputed election in the former Soviet republic.
Kuchma was expected back in Kiev for talks later on Thursday with Ukraine's two rival presidential camps.
Putin openly backed pro-Moscow Prime Minister Viktor Yanukovich in a disputed 21 November election and has since sparred with the West over the political crisis engulfing its western neighbour.
Schroeder spoke to Putin over
the phone on the Ukraine issue
The Russian leader was also the first to congratulate Yanukovich with a victory that is now under review by Ukraine's supreme court.
Meanwhile, a German government spokesman reported on Wednesday that Chancellor Gerhard Schroeder and Putin agreed in a telephone conversation that the outcome of any new presidential election in Ukraine "must be strictly respected".
Kuchma held round-table talks on Wednesday in Kiev with Western mediators and the rivals to replace him: the pro-Western opposition leader Viktor Yushchenko and Yanukovich.
Yushchenko has refused to concede defeat in the election and is demanding a quick re-vote of the 21 November poll in which he would face off against Yanukovich.
New vote urged
Yushchenko also dismissed Kuchma's previously unscheduled trip to Russia.
"The source of power is in Ukraine - it is the people," the opposition leader told reporters.
Meanwhile, one of his top deputies has demanded that a new vote be scheduled by the weekend.
"We will not allow the process to drag on. We want an agreement on the necessary changes within 24 or 48 hours"
senior opposition figure
"We will not allow the process to drag on. We want an agreement on the necessary changes within 24 or 48 hours," senior opposition figure Yulia Timoshenko told reporters.
"The opposition demands that amendments be urgently submitted to the law on presidential elections in order to clearly fix a date for a new second round," she said.
However, Kuchma has said he would prefer to stage the election from scratch, meaning that other candidates could enter the race which would take several months to prepare.
This would allow the ruling party to select a new candidate should it feel that Yanukovich will be unable to beat off the opposition again.