The Malaysia Today site however remains accessible through an alternative link.
An official from the commission, speaking on condition of anonymity, said the site was deemed to have broken the law, adding that a formal statement with details will be issued later.
Malaysia Today is run by Raja Petra Kamarudin, a prominent local blogger known for his stinging political comments on the internet who regularly publishes numerous claims about alleged wrongdoing by government leaders.
"Blocking my site is a move by a desperate government that is trying to silence me, but it's not going to stop me," he told The Associated Press.
"It only reveals that the government does not know how to handle the Internet."
Government officials have repeatedly accused Raja Petra of spreading malicious falsehoods through his blog.
"Everyone is subject to the law, even websites and blogs"
Syed Hamid Albar, home minister
He is already facing charges of sedition and criminal defamation over an article and a sworn statement he made alleging links between the country's deputy prime minister and a murdered Mongolian woman.
The trial begins in October.
In defending Wednesday's order, Syed Hamid Albar, the home minister, said: "Everyone is subject to the law, even websites and blogs."
He said the government does not "intend to curtail people's freedom or right to express themselves".
"But when they publish things that are libellous, slanderous or defamatory, it is natural for [authorities] to act," he was quoted as saying by The Star newspaper, a leading local English daily, on its website.
A court earlier this month ordered Raja Petra to reveal the sources for articles alleging sodomy accusations against an opposition leader.
The crackdown on Malaysia Today also drew criticism from bloggers and journalists who accused the authorities of seeking to deter dissent.
Wong Chun Wai, a senior editor at The Star newspaper, said the order was "myopic and ridiculous" and went against the government's promise not to censor the internet.
"If it can happen to [Raja Petra], it can also happen to other bloggers," he wrote on his blog.
"In a democracy, we don't have to agree with each other but we must defend the right of everyone to speak up, including [Raja Petra] and other voices of dissent."
Some of Malaysia's most popular websites and blogs offer fiercely anti-government commentaries, presenting themselves as an alternative to mainstream media, which are controlled by ruling political parties or closely linked to them.