Kyiv had suggested the attack came from Russia as fears persist that Moscow is planning to invade its Western-backed neighbour Ukraine.
"We do not know anything. As expected, Ukraine continues blaming Russia for everything," Kremlin spokesman Dmitry Peskov told reporters.
"Russia has nothing to do with any DDOS attacks," Peskov added.
The affected sites included the Oschadbank state savings bank and Privat -- two of the country's largest financial institutions.
Both resumed service later on Tuesday but the military sites remained inaccessible hours after the initial reports of the attack emerged.
Ukraine's communications watchdog pointed the finger at Moscow.
"It cannot be excluded that the aggressor is resorting to dirty tricks," the watchdog said in reference to Russia.
Tuesday's cyberattack came one month after another strike briefly took down key government websites.
NATO responded within hours of the January attack by announcing a cyber warfare cooperation deal with Kyiv. The European Union also said it was mobilising "all its resources" to help Ukraine at the time.
Kyiv said the damage in January had been limited and held back on apportioning blame.
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