The site, run by the commission in charge of organising Sunday's election, briefly shut down.
Ukrainian security officials blamed a denial-of-service (DDoS) attack, a method that can slow down or disable a network by flooding it with communications requests.
"There is a DDoS attack on the commission's site," the government information security service said on its Facebook page.
The security service said the attack was "predictable" and that measures had been prepared in advance to ensure that the election site could not be completely taken down.
"If a site runs slowly, that doesn't mean it has been destroyed by hackers," the statement said.
A report on Russia's state news agency RIA Novosti quoted a statement on the personal website of the Ukrainian prosecutor general saying that the electronic vote counting system was out of order and that Sunday's ballots would have to be counted by hand.
The commission spokesman, Kostyantyn Khivrenko, called the RIA Novosti report a "fake".
"The Central Election Commission will issue preliminary results of the voting with the help of the Vybory information-analytical system. This system is working normally," he said.
The Ukrainian Security Service (SBU), the country's lead internal security agency, said that "the physical protection of the central server and its regional components has been ensured".
"Any statements regarding the alleged successful unauthorised intrusions into the cyber space of the Central Election Commission or the elements of the elections systems do not correspond to the facts. Hackers are controlling nothing," Markiyan Lubkivskyy, an adviser to the SBU chief, said.
An SBU spokeswoman told AFP that attacks on the election commission's site began a week ago, "but so far we have dealt with them".
Outdoor video screens hacked?
The cyber troubles came as Ukraine prepared for an election overshadowed by a bloody pro-Russian insurgency in the country's east and the annexation by Russia of the Crimean province in the south.
Pro-Western and nationalist parties are expected to dominate the new parliament.
In another possible sign of cyber tensions, the Ukrainska Pravda news website on Friday reported that outdoor video screens across Kiev were briefly hacked.
The screens, which are used for advertising, including pre-election political ads, reportedly started to display "scary and horrible images," the report said.
Engineers went out "to physically unplug" the screens, according to the report.
The report could not be confirmed, but footage on YouTube purporting to capture the incident showed a street screen abruptly switching to footage of destroyed buildings and dead bodies, as well as the images of two nationalist politicians running for parliament, with the words "war criminals".