The websites of Israel's military, Mossad and the Shin Bet intelligence services were back online on Monday after being unavailable the previous day due to what officials said was a "server crash."
The three sites, along with numerous other government websites, crashed on Sunday, two days after the international hackers' group Anonymous apparently threatened to take action after Israel blocked two boats of pro-Palestinian activists from reaching the blockaded Gaza Strip.
All three sites appeared to be working normally on Monday after being unavailable all day on Sunday.
A spokesman for the office of Prime Minister Benjamin Netanyahu, whose website was not affected, blamed the outage on a "server malfunction" technical glitch rather than an attack by hackers.
"Israeli government websites crashed today because of a server malfunction, not as a result of a cyber attack," Ofir Gendelman wrote in a posting on Twitter late on Sunday.
The sites went down shortly after a video was posted on YouTube, allegedly by "hacktivist" group Anonymous, in which they threatened the Israeli government with retaliation after Friday's interception of two activist vessels which had been hoping to run Israel's naval blockade on the territory.
An earlier attempt to run the Gaza blockade in May 2010 had ended in bloodshed when Israeli naval commandos stormed the lead vessel of a six-ship flotilla, killing nine Turkish activists and sparking a wave of international condemnation -- and a flurry of new attempts to reach the coastal enclave.
Entitled "An open letter from Anonymous to the Government of Israel," the video accused the Jewish state of "piracy on the high seas" and warned that if it continued to block ships heading to Gaza "then you will leave us no choice but to strike back," it said.
It was not immediately possible to confirm whether the video was posted by Anonymous, which has been involved in scores of hacking exploits, many of them targeting governments.
Last year, hackers associated with Anonymous launched retaliatory attacks on companies perceived to be enemies of the anti-secrecy website WikiLeaks.