The raid prompted protests in Stockholm
The row between supporters of a Swedish website accused of piracy and the nation's authorities is escalating.
A raid on The Pirate Bay site by Swedish police is thought to have been the catalyst for hack attacks on official websites.
The attacks are being investigated by the Swedish security service, its domestic intelligence agency.
Protestors took to the streets of Stockholm on Saturday to show their support for the BitTorrent search site.
The Swedish government website was unavailable late on Saturday following an attack that, it is thought, was related to the raids on The Pirate Bay.
Although never entirely offline, the site was hard to reach for about nine hours, a government spokesman said.
The Pirate Bay describes itself as a search site for BitTorrent, a net technology that lets people share large files over the net.
It was raided by police amid claims that it was giving people access to copyrighted material.
Some 200 servers were seized and three men arrested in the action.
The day after the raids, the website of Sweden's police force was knocked offline.
The Security Police intelligence agency is now investigating both attacks.
Other official bodies in Sweden, including 21 local authorities and 31 organisations that deal with emergencies, were told to beef up defences on their websites to ward off attacks.
The Pirate Bay, which claims to have more than a million registered users, was back up and running soon after the raids as servers were moved to the Netherlands.
In 2005 Sweden passed laws that ban the downloading of copyrighted movies and music but the country is also home to a sizeable group who believe the net should give people free access to media files.
Several hundred of these people staged a protest in Stockholm on Saturday to highlight what they saw as heavy-handed tactics by the nation's police forces.
Protests also came from other firms caught up in the raids.
Game Switch, which provides servers to support online gaming, said the police had mistakenly seized its hardware when it took action against The Pirate Bay.
"As a result of this seemingly irrational and disproportionate move by police, our entire business, in effect, has also been seized," said Christopher Adams, GameSwitch director in the statement.