Daily Mail reported that the hacker known only by his alias TinKode, published online details which he recovered from the site, including the user names and passwords of the site's administrators.
The shocking breach comes just weeks after the Government used last month's Strategic Defence and Security Review to make countering cyber-warfare a priority.
The Navy has confirmed that the website had been hacked, but stressed that no classified information had been accessed or disclosed. It also said that security teams are investigating how the hacker infiltrated the site, which has been suspended temporarily as a precaution.
The hacker, who has previously disclosed similar attacks on NASA and U.S. Army websites, reportedly gained access to the website on Friday.
The paper quoted Graham Cluley, a senior security analyst, as saying that the incident was 'immensely embarrassing,' and "now we have the Royal Navy with egg on its face".
"He's more of a show-off type of hacker rather than malicious. But if he'd wanted to he could have inserted links which would have taken readers to malicious site," he added.
TinKode hacked into the Navy's blog, Jackspeak, and to an area called Global Ops, the paper added.