The men, aged 17 and 42, were arrested following a complaint lodged by the website administrators of the Istana, the official residence of President Tony Tan.
The website was hacked and displayed a crude image in the early hours of November 8, about an hour after Prime Minister Lee Hsien Loong's website displayed mocking messages and pictures from activist hackers' group Anonymous.
Police said the two attacks are unrelated to each other.
The suspects in the Istana website hacking will be charged in court tomorrow for offences under the city-state's Computer Misuse and Cybersecurity Act.
Police did not reveal the identity of the two suspects, but Singaporean businessman Doolson Moo last week revealed to the Straits Times newspaper that he was the one who penetrated the Istana website to "test for vulnerabilities".
The 42-year-old said he entered a line of computer code into the search box on the website that allowed him to display a picture of an old woman pointing her middle finger, along with a string of offensive words in the southern Chinese dialect of Hokkien.
The arrests today come after another Singaporean, 35-year-old James Raj, was charged in court on November 12 with hacking a municipal council's website and posting an image of a Guy Fawkes mask, the international symbol of Anonymous.
The council is located in a district represented by the prime minister.
A man claiming to speak for Anonymous has demanded that Singapore scrap a law requiring news websites to obtain annual licences.
The new Internet licensing rules came into force in June and have angered bloggers and activists who say they are designed to muzzle free expression.
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