Malaysiakini CEO Premesh Chandran said that this was the second time the award-winning online paper had experienced an attack on their system this month.
A fortnight ago, the paper had repelled a hacker's attempt to break into their system. "I don't think the hacker was successful because so far we haven't detected anything out of the ordinary," he told AFP.
Chandran said he had no idea who was behind the attacks. "It could just be a prankster, but if it was a more sinister source it could be very dangerous," he said.
Malaysiakini, which was started in 1999, has been accused of a pro-opposition bias by the authorities. Its reporters have on occasion been banned from attending official events.
Malaysia is tightening up its laws concerning the Internet. It already has laws which punish "malicious reporting" by conventional media with jail, or by restricting their circulation.