The Western military alliance's spokeswoman, Oana Lungescu, said on social networking site Twitter that cyber attacks, which began on Saturday evening, continued on Sunday, although most services had now been restored.
"It doesn't impede our ability to command and control our forces. At no time was there any risk to our classified networks," another NATO official said.
NATO's main public website (www.nato.int), which carried a statement by Secretary-General Anders Fogh Rasmussen saying that Sunday's referendum on Crimea's status would violate international law and lack legitimacy, worked intermittently, Reuters reported.
The so-called "distributed denial of service" (DDoS) attack, in which hackers bombard websites with requests causing them to slow down or crash, also hit the site of a NATO-affiliated cyber security center in Estonia. NATO's unclassified e-mail network was also affected.
A group calling itself "cyber berkut" said the attack had been carried out by patriotic Ukrainians angry over what they saw as NATO interference in their country.
The claim, made at www.cyber-berkut.org, could not be independently verified. "Berkut" is a reference to the feared and since disbanded riot squads used by the government of ousted pro-Russian Ukrainian President Viktor Yanukovich.
Cyber warfare expert Jeffrey Carr, in a blog on the attacks, described cyber berkut as staunch supporters of Yanukovich and a "pro-Russia hacktivist group working against Ukrainian independence".
Lungescu noted the statement by "a group of hacktivists" but said that, due to the complexities involved in attributing the attacks, NATO would not speculate about who was responsible or their motives.