The Jerusalem Post said Internet sites of the Israeli armed forces, Shin Bet, Mossad, and the Health and Interior ministries were all unavailable to visitors.
Anonymous posted a video on YouTube vowing to hack Israeli Web sites to protest the Israeli navy's interception of two boat-loads of activists bound for the Gaza Strip.
An Israeli military spokeswoman, however, cited the Tehila Internet firm that operates the government Web sites in telling the Post the interruption was the result of "server error."
The Tel Aviv newspaper Haaretz reported the Israeli military and Shin Bet said they were investigating the malfunction. Security officials said the problem only affected external government sites, not the agencies' internal computer networks, Haaretz said.
Anonymous also threatened to disable Web site of the Israeli parliament, the Knesset, a few months ago, the newspaper said.