 Thousands of copies of the Standard were burnt |
Internal Security Minister John Michuki said the raids on the Standard group in Nairobi were to protect state security.
"If you rattle a snake, you must be prepared to be bitten by it," he said, amid protests by opposition MPs.
Three Standard journalists are still being held without charge following a story about President Mwai Kibaki.
Both the president and senior opposition figure Kalonzo Musyoka deny a report in the Standard last week that they had been holding secret meetings.
 |  Energy and resources being used to crack down on the media need to be channelled toward the fight against corruption  Eddie Mandhry, New York  |
The BBC's Karen Allen in Nairobi says the raids are being seen as an indicator of growing political tension in an administration facing charges of corruption.
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 as "acts of thuggery [that] have no place in an open democratic society".
In a statement, it said: "We note that these attacks were preceded by threats directed against the Standard from representatives of the Kenyan government."
It urged the government to stop its "campaign of vilification and harassment of selected media".
Police accused
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.
 Three Standard journalists are still being held |
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.
Meanwhile, another group of masked men went to the offices of the independent Kenya Television Network (KTN), a sister to the Standard.
The station was off air until 1100GMT, and men carried away computers and transmission equipment, and detained four staff members.
Investigation
Opposition MPs joined by more than 100 demonstrators marched from parliament to outside the Standard's offices in protest at the raids, which Standard group Chief Executive Tom Mshindi had condemned earlier.
"If it is confirmed the action was sanctioned by the government, it would reflect badly on our country's claims to democracy and freedom of the media," he said.
 President Kibaki's government has been rocked by graft allegations |
Information Minister Mutahi Kagwe, a former Standard editor, initially denied any knowledge of the raid, saying he first learnt about it on television news reports.
Kalonzo Musyoka, the former environment minister who was sacked after opposing a proposed new constitution and is named in the now controversial newspaper report, condemned the raids.
"This is a very very dark morning for this beautiful country," he said.
The newspaper has been critical of President Kibaki's handling of recent corruption scandals.
The three Standard journalists, Chaacha Mwita, Dennis Onyango and Ayub Savula were arrested on Tuesday following the publication of the most recent article.
The government has repeatedly accused the Standard of fabricating stories.
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