Stephen Woloshyn, a monitor, said he saw more than 10,000 blank ballots at an election office in the eastern town of Donetsk.
"They are trying to add 10,000 votes to the list - which is illegal," said Woloshyn, an election monitor from the Canadian-Ukranian Association.
Vote-rigging led to the 2004 presidential election result being annulled and Viktor Yushchenko sweeping to power after the 'Orange Revolution.'
Polls had opened at 7am (04:00 GMT) and closed at 10pm (1900 GMT).
No clear winner is expected and protracted coalition talks to form a government are almost certain.
Laurence Lee, Al Jazeera's correspondent in Donetsk, said allegations of vote rigging were coming in from other parts of the country.
"There is potential for this to go to the courts and that could take week and weeks to resolve."
Ukranians have faced three years of political paralysis as Yushchenko has sought to push his Moscow-backed rival from power.
Viktor Yanukovych was forecast to win the most votes with his Regions Party.
He said Ukraine was "being put to the test," and warned he would not recognise the results in the case of "total lawlessness" in the poll.
But Yushchenko hopes an alliance with Yulia Tymoshenko, his partner in the "Orange Revolution," will enable him to form a coalition government and remove Yanukovych from power.
"I am convinced that today the nation will choose change," Yushchenko said after voting in central Kiev.
Yushchenko defeated Yanukovych in a re-run of the presidential election in 2004 after the original result was declared invalid following a series of mass pro-democracy protests that became known as the Orange Revolution.
Since then however, Yushenko has failed to implement many of the reforms he promised and Yanukovych, who favours closer ties with Russia, has undergone a political resurrection.
After being accused of rigging the presidential vote in 2004, he became prime minister after his party won a majority in elections in 2006.
Yushchenko is pinning his hopes on a last-minute alliance with Tymoshenko - a partnership that could give their parties control of parliament, even if Yanukovych's bloc wins the most votes on Sunday.
Forging a government coalition with Tymoshenko, however, could mean weeks of negotiation between their two parties, and Yanukovych has signalled that he would not give up power easily - threatening protracted election uncertainty.
Yanukovych, who draws his support from Ukraine's Russian-speaking east and south, fiercely resisted Yushchenko's decision to dissolve parliament in April and call new elections after the president accused him of seeking to seize power.
Yanukovych eventually agreed to the vote on Sunday, but has suggested victory would be the only outcome he is prepared to accept.
Ukraine has 37.5 million registered voters but irregularities in voter registration has increased fears there could be legal challenges to any result.