The Haaretz daily reported Monday that the shutdown was the "biggest computer crash in the history of Israel's online government."
The Web sites of the armed forces, the Mossad foreign intelligence agency and the General Security Service, Israel's internal security branch known as Shin Bet, and several government ministries broke down Sunday.
Authorities denied there had been a cyberattack and blamed a "malfunction" in "the IBM-manufactured storage component" of the government computer system.
The sites were down for several hours.
There was skepticism about the official explanation because the breakdown occurred just days after Anonymous, a shadowy group of global hackers and online activists, threatened to retaliate against Israel for its maritime blockade of the economically crippled Gaza Strip.
In a YouTube video posted Friday, the group accused Israel of "piracy on the high seas" for intercepting two ships -- one Canadian, one Irish -- carrying humanitarian aid for the Gaza's beleaguered 1.2 million Palestinians in international waters earlier that day.
Israeli naval commandoes boarded the ships and took them to the port of Ashdod in southern Israel.
"Your actions are illegal, against democracy and human rights, international and maritime law," a computer-generated voice declared on the video.
"If you continue blocking humanitarian vessels to Gaza … then you leave us no choice but to strike back again and again until you stop."
There was no way to authenticate the video. Anonymous threatened Israel in June, although there's no record of a cyberattack before Friday.
Anonymous, which claims to fight for human rights and against Internet censorship, has carried out cyberattacks on several governments and international conglomerates since 2008. During the Arab Spring pro-democracy uprisings in Egypt, Tunisia and Syria it repeatedly paralyzed government Web sites to support the protesters.
Suspected Anonymous activists have been arrested in a half a dozen countries, including Britain, Australia and Turkey.
The Israeli security establishment has been building a cyberdefense apparatus for some time. But in September, reservist Maj. Gen. Yiftach Ron-Tal, chairman of the Israel Electric Corp., warned the cyberthreat to Israel is growing but that the country isn't adequately prepared to cope with it.
He raised the possibility that Israel's enemies had already implanted viruses in its computer systems that control military and civilian infrastructure like the defense industry and the national power grid.
Israel's military is digitalized down to platoon level and thus becomes vulnerable to cyberattack during combat.
Israel's water, transportation and financial systems, as well as its military command network, face potential cyberattacks.
Ron-Tal, a former commander of Israel's land forces, declared: "We could already have witnessed a silent infiltration that will be activated when the enemy wants.
"We need to be prepared for the possibility that critical infrastructure will be paralyzed."
Sunday's shutdown, if it was a cyberattack, came amid growing tensions over Iran's nuclear program and increasing speculation that Prime Minister Binyamin Netanyahu was pushing for pre-emptive strikes against the Islamic Republic.
Israel's intelligence establishment has been widely blamed for sabotaging Iran's nuclear program in 2010 with a malignant virus known as Stuxnet. The Iranians claim their systems were hit later by another virus they dubbed "Stars," and blamed Israel again.
Since then the Iranians have made a major effort to build up cyberdefenses and the capability to retaliate.
Little is known of the status of these efforts but the possibility of payback against Israel is clearly a strategic objective for Tehran in the emerging cyber battlefield.
Iranian Gen. Ali Fazli, commander of the Revolutionary Guard's paramilitary Basij organization, claimed in March that Tehran has launched attacks against the Web sites of "the enemies."
The Jerusalem Post reported in August that Israel's military had set up a cyberdefense division, primarily to counter any Iranian threat, within the C4I -- command, control, communications, computers and intelligence -- Directorate.
That move followed Netanyahu's announcement in July that a National Cybernetic Task Force had been established to defend the country's vital infrastructure from Internet strikes.