The services have been down since Monday afternoon when water leaked into the server room at the Finance Ministry in the European Union member.
An inquiry has been ordered into why the sensitive electronic equipment had not been moved following a cabinet decision to do so in November.
The leak meant all government websites, emails and online services were disconnected as a precaution.
Officials could not say when government services will be back online. The government call centre had been restored and was operational, however.
"Unfortunately, the systems were placed at the Finance Ministry in a way that exposed them to a possible accident, even though the cabinet decided in November 2022 to move the equipment," an official statement said.
Government spokesman Konstantinos Letymbiotis said the probe would cover whether measures to protect the equipment had been taken at the server site.
"The positive thing is that data has not been lost, so once the servers are restored, the government's websites and email systems can gradually start functioning," he told reporters.
The Cyprus land registry department had only recently resumed normal operations after being knocked out for several weeks by a hacking attack on its systems.
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