In a major embarrassment to Israeli security agencies, their websites crashed barely two days after a hacker group threatened to paralyse the Jewish state's online activities over the interception of two Gaza-bound ships trying to break the blockade of the coastal territory.

All Israeli government and security-related websites that crashed on Sunday started working once again overnight after long hours of malfunctions.

The international hackers' group Anonymous had earlier threatened the government in response to the Israel Navy's interception on Friday of two boats of activists trying to reach Gaza, but Israel's e-Government, responsible for managing the state's websites, denied claims that they were hacked.

Among the sites that were affected were those of the Israel Defence Forces (IDF), the Shin Bet security service and the Mossad, Israel's espionage agency.

"A thorough investigation was conducted and the source of the malfunction was found to be IBM-manufactured storage component," e-Government said in a statement.

"During the night, e-Government worked with IBM representatives to restore the component successfully," it said.

The release said that that they will continue to thoroughly investigate the malfunction in order to be able to prevent similar incidents in the future.

The fact that the biggest computer crash in the history of Israel's online government came so soon after the 'Anonymous' threat led many to greet the treasury claim with scepticism.

The hacker group is credited with paralysing the web activity of numerous governments and large companies all over the world.

The threat, issued in an online video addressed directly to the Israeli government, called the interception of the activists' vessels an act of "piracy" and an "illegal action against human rights, democracy and international and maritime laws."

The group said that if Israel continued to prevent "humanitarian" missions and continued its "crimes against unarmed civilians," the group would "have no choice but to strike back, again and again."

A short time after the video was uploaded, the government sites crashed.