Israeli officials and security experts have rejected claims that a cyber-attack by the hacker group Anonymous was behind the failure of several government websites on Sunday, including those of the Mossad, the Shin Bet secret service, the Israeli army and some government ministries.

The websites were inaccessible for several hours but all were back online again by Monday.

In a YouTube video posted last Friday, Anonymous threatened to "strike back" at Israel if it continued to block vessels attempting to reach Gaza by sea. The video was released shortly after Israeli naval commandos boarded a Canadian and Irish vessel sailing to Gaza and arrested the passengers and crew.

In the YouTube message An Open Letter from Anonymous to the Government of Israel, an electronically generated voice can be heard accusing Israel of "piracy on the high seas". "Your actions are illegal, against democracy, human rights, international, and maritime laws," the statement continues. "Justifying war, murder, illegal interception, and pirate-like activities under an illegal cover of defence will not go unnoticed by us or the people of the world.

"We do not tolerate this kind of repeated offensive behaviour against unarmed civilians. If you continue blocking humanitarian vessels to Gaza or repeat the dreadful actions of 31 May 2010 against any Gaza freedom flotillas then you will leave us no choice but to strike back. Again and again, until you stop." The message ends with a warning: "Expect us."

The Israeli sites crashed about 48 hours later. An army spokesperson said it was "a coincidence" – a response dismissed by observers who noted that several Palestinian sites were hacked last week, as was the site of the Russell tribunal, currently hearing testimony in South Africa on why Israel is an apartheid state.

But Nitzan Miron, a former member of Matzov, the cyber security division of the Israeli military, responsible for defending networks from hackers, said the breakdown was "a really strange coincidence".

Miron, now chief executive of 6Scan, a website security start-up in Tel Aviv, said there had been a hardware crash rather than a software problem caused by a cyber-attack. "Nothing is impossible but it doesn't look like it [a cyber-attack]," he said. He said a decision to group all the sites in one hardware system had resulted in a chain reaction of malfunctions.

"It's all part of a project called Tehila that puts all of those sites together in one data centre. When one fell, they all fell. The back-ups failed. Hopefully next time they'll have better back-ups and this kind of thing shouldn't happen," he said. "Those were just the front-end sites. They don't contain the actual classified information."

The successful penetration of some of Israel's most prominent sites would be a major embarrassment to the Israelis, who pioneered cyber security and whose algorithms protect large swaths of computerised banking and e-commerce around the world.