The Kenyan government has confirmed it ordered police to raid the offices of a newspaper and its sister TV station.
Thousands of copies of the Standard were burnt
Armed and masked men stormed the HQ and printing presses of the Standard group, owner of the Standard newspaper and the Kenya Television Network.
Thousands of copies of the paper were burned, but the TV station is now back on air after being shut down for hours.
The newspaper has been critical of President Mwai Kibaki's handling of recent corruption scandals.
The government has repeatedly accused the Standard of fabricating stories.
Internal Security Minister John Michuki said the raids on the Standard group in Nairobi were designed to protect state security.
"If you rattle a snake, you must be prepared to be bitten by it," he said.
The BBC's Karen Allen in Nairobi says the raids are being seen as an indicator of growing political tension in the administration.
Three ministers have resigned this year after details of a corruption investigation were leaked to several newspapers.
The US embassy in Nairobi has condemned the raids.
In a statement, it said it deplored the "campaign of vilification and harassment" of some media.
"These acts of thuggery have no place in an open democratic society," it said.
Three Standard journalists have been freed on bail
Opposition MPs and other demonstrators marched from parliament to the Standard's offices in protest.
Opposition leader Uhuru Kenyatta described the action as a "dark day" for Kenya.
Three Standard journalists have been charged with publishing alarming statements following a story about President Kibaki and released on bail.
Both the president and senior opposition figure Kalonzo Musyoka have denied a report in the Standard last week that said they had been holding secret meetings.
Police Commissioner Jasper Ombati said he had evidence that journalists were being paid to incite ethnic hatred.
He said that police officers routinely wore masks to hide their identities in sensitive cases.
Hooded men carrying AK-47 assault rifles raided the headquarters of the Standard group just after midnight.
Staff were kicked and beaten and forced to lie on the floors as offices were searched and equipment taken away, the Standard newspaper said on its website.
"They kicked us as we went down, they frisked our pockets and took our belongings," one member of staff said.
A similar raid was carried out about an hour later at the group's newspaper presses in the capital's industrial area.
Thousands of copies of Thursday's edition of the newspaper were dragged out into the yard and set on fire.
The police denied their officers were responsible for burning the papers and promised to investigate.
Meanwhile, another group of masked men went to the offices of the Kenya Television Network.
The station was off air until 1100 GMT, and men carried away computers and transmission equipment. Four staff members were detained.
Later, Information Minister Mutahi Kagwe said the government remained "committed to the ideal of press freedom and promotion of responsible journalism".