The raid, the first of its kind by authorities on a mainstream media outlet since independence from Britain in 1963, sparked a wave of domestic and international protests.
Police later defended their actions and said they had acted in the interests of national security. Officers accuse employees of the Standard Group had taken bribes to write stories in order to provoke instability.
Computers were seized and transmission equipment of the independent Kenya Television Network (KTN) also confiscated as dozens of policemen stormed the offices armed with AK-47 assault rifles shortly after midnight Thursday.
Witnesses alleged that during the raid, police damaged the Standard newspaper's press and set alight thousands of copies of Thursday's newly-printed edition.
Information minister unaware
Information Minister Mutahi Kagwe told journalists he did not order the raid and knew nothing about it. A government spokesman promised to hold a news conference later in the day.
Ezekiel Mutua, secretary-general of the Kenya Union of Journalists, said that the raid was designed by the government to create free among journalists and punish the Standard Group.
"This is quite shocking. It is the most outrageous and sinister act against the media we have seen," Mr Mutua.
He said the newspaper group received no complaints regarding stories it printed through the normal channels, the Media Council of Kenya.
Controversial report
On Thursday, three Standard journalists were charged in court for offences linked to a news story that claimed President Mwai Kibaki had held secret talks with a fierce rival, former minister Kalonzo Musyoka, a politically volatile assertion denied by both parties.
The trio pleaded not guilty and was released on bail. The paper rejected government demands to print a retraction and apology.
Police briefly detained four KTN employees and confiscated video tapes and mobile telephones during the raid, staffers allege.
International outrage
In a joint statement, a host of senior diplomats from across the European Union, as well as from the United States, Australia, Canada and Japan, condemned the raids. The statement described it as "an unacceptable attack on the freedom of the press... unprecedented in Kenya”.
The diplomats called on Nairobi to openly investigate reports of "assault, theft, unlawful destruction of property, kidnapping and harassment."
Kenyan police also issued a statement, saying they had "conducted an operation at the Standard Group premises to collect evidence of an intended act (which) would have posed a major threat to national security."