Internet users who visited the National Board of Health and Welfare's official website were greeted by a warning of further attacks and profanity against the government, the Swedish news agency TT reported.
The country's Courts Administration website was crippled by a similar attack early Wednesday.
"We're looking into it," Courts Administration spokesperson Hakan Sonesson said. "There's definitely a disturbance but we have no details yet about what's lying behind this."
A video posted by Anonymous on YouTube warned of future attacks.
"Swedish government; you know our capabilities and what we want! The choice is yours," a masked spokesperson said.
A series of denial of service attacks hit Sweden Monday, paralyzing the websites of several banks, the news agency TT and a number of government agencies.
The head of the country's computer security team said there is little organizations can do to protect themselves against denial of service attacks.