The Internet and phone regulator IDA said Prime Minister Lee Hsien Loong's official site was compromised late Thursday night, Todayonline reported.
A section of the Istana website -- the site of President Tony Tan's official residence -- was hacked into at around 12.20 a.m. this morning [Nov. 8].
Despite the hacking, the main sites remained working and an investigation is under way, IDA said.
"We will continue to strengthen all government websites," IDA said. "This includes the checking and fixing of vulnerabilities and software patching. While this is in progress, visitors to government websites may experience intermittent problems with access. This will be completed as soon as possible."
The IDA statement didn't name the hackers or source of hacking, but said they used the sites' cross-site scripting to display pages from other sources.
The BBC reported the hackers had posted an image of a Guy Fawkes mask -- which was popularized in the comic series and movie "V for Vendetta" and became the symbol of the global hacker-activist group Anonymous -- on the PM's website with the words, "It's great to be Singaporean today."
Fawkes was a Catholic who failed to blow up the British House of Lords in 1605. The mask is believed to have been used first by Anonymous in 2008 during a protest against Scientology.
The BBC report said the hacked website pages displayed mocking messages and pictures from Anonymous, which is demanding the scrapping of rules requiring Singaporean news websites to obtain an annual license.
Some bloggers and media activists claim the rules, which came into effect in June, are crushing free expression.
Todayonline reported that the two hacks come after hackers threatened last week to cripple Singapore's information technology infrastructure.
Lee warned hackers Wednesday that authorities would "spare no effort" to track down anyone threatening the government's IT infrastructure, Todayonline reported.
Singaporean government agencies have been on alert against hacking since early this month when someone claiming to be part of Anonymous posted an online video threatening the country's infrastructure.
The Straits Times reported that the Government IT Security Incident Response Team had alerted all government agencies after the video was posted on YouTube.
In the United States, prosecutors in Virginia charged 13 suspected Anonymous members in October for conspiring on cyber attacks targeting Mastercard and Visa, as well as anti-piracy groups, such as the U.S. Copyright Office and the Recording Industry of America.
The Washington Post reported that the attacks occurred in 2010, when Anonymous members reportedly retaliated for the shutdown of Pirate Bay, a Swedish file-sharing site.
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