The "distributed denial of service" attacks flooded the websites with traffic, forcing them offline about 5.20pm yesterday.
As of this morning, service to both websites has been restored.
The attacks may be related to the Global Atheist Convention, which is being held in Melbourne in March next year. Speakers include Richard Dawkins, author of The God Delusion and comedy writer Catherine Deveny.
About 1000 tickets have been sold so far through the Global Atheist Convention website, which was set up, and is operated, by the AFA.
The AFA is billing the event as the largest gathering of atheists in Australian history but ticket sales have had to be halted for now due to the cyber attack.
David Nicholls, president of the AFA, said it was not yet clear whether the attacks were motivated by religion or conservative Christian groups' anger at the AFA's lobbying for a more secular society.
However, the fact that two separate atheism-related websites were hit suggested the attack was targeted at atheists.
"We have been informed that the Atheist Foundation of Australia and the Global Atheist Convention sites were the specific target of the attacks," Nicholls said, adding he had reported the incident to the Australian Federal Police.
"This may not be just an attack on atheism, but an attack on freedom of speech."
"Our aim is to keep the Australian government, education and welfare systems secular," Nicholls said.
"Unfortunately, some people in our society find that very confronting."
The cyber attacks are reminiscent of last year's major attacks on Scientology websites by a group of loosely connected online miscreants that called themselves Anonymous.
In May this year, 19-year-old Dmitriy Guzner from New Jersey agreed to plead guilty to playing a part in the attacks, which crashed Scientology websites. The final outcome of the case is not clear but he faced up to 10 years in prison.