The Mossad and Shin Bet intelligence services, the military spokesman and the Interior Ministry are some of those which have closed.

A spokeswoman for Shin Bet said: “We can confirm that the website has been down for several hours and an investigation is ongoing. Initial investigations conducted by Tehila, the Internet company, indicate problems with the website servers.”

In response to speculation that hackers were responsible, the Israeli government released a statement saying the problem “was not a cyber attack but only a technical malfunction”.

The statement added that the problem was “currently being dealt with by experts”.

The crash came two days after a warning was posted on YouTube in the name of the cyber “hacktivist” group Anonymous, threatening retaliation after the Israeli navy stopped two boats from travelling to Gaza on Friday.

The boats, which were carrying 27 journalists, crew and peace activists from Ireland, Canada, the United States, Australia and Palestine, were stopped in international waters.

The warning said: “If you continue blocking humanitarian vessels to Gaza or repeat the dreadful actions of May 31st, 2010 against any Gaza Freedom Flotillas then you will leave us no choice but to strike back.”

Last week after Palestine won full membership of UNESCO, hackers attacked Palestinian servers to cut Internet service across the West Bank and Gaza.