"It has nothing to do with an attack, no threat and no hacking. It's just a system malfunction," Zvi Slater, the deputy director of the government's Information Technology Unit, told Ynetnews.com. "Our best minds are working to fix the problem. They were not hacked."
The Web sites of the Israel Security Agency (Shin Bet), the Mossad, the army and the army's spokesman's office were among those affected. Channel 1 television said no sensitive material was jeopardized.
Government ministries including the Construction and Housing Ministry, the Health Ministry, the president's official Web site and that of Israel Atomic Energy were also affected, Ynetnews.com said.
All the sites were up and running Monday.
A video uploaded Friday on YouTube by Anonymous warned it would strike back after Israel prevented a two-boat flotilla from reaching Gaza.
"We do not tolerate this kind of repeated offensive behavior against unarmed civilians. If you continue blocking humanitarian vessels to Gaza … then you will leave us no choice but to strike back again and again until you stop," Ynetnews.com quoted a computerized voice saying on the video.