Kenya's Standard newspaper came out as normal a day after its offices were stormed by police and its sister television station taken off air.
Protests against the raids were held outside the Standard offices
The raids have provoked national and international condemnation. Nearly 30 diplomats called it an unprecedented attack on press freedoms.
The action appears to have split the cabinet, with one group of influential ministers denouncing it as "barbaric".
The internal security minister said it was designed to protect state security.
"If you rattle a snake, you must be prepared to be bitten by it," John Michuki told reporters on Thursday.
Masked and armed police moved in on the Standard's offices and printing presses in the early hours of Thursday.
They seized tapes and destroyed equipment. Thousands of copies of the newspaper were burned.
A similar raid was carried out at the Kenya Television News (KTN) station.
Kenya's other leading daily, the Nation, reported that several ministers - including Local Government Minister Muskari Kombo and Health Minister Charity Ngilu - were furious at the raids.
They have demanded that those who authorised the action be identified and punished, the paper said.
"I believe in the freedom of the press," Mr Kombo said on Thursday. "I have in the past been unhappy with irresponsible journalism, but that... is not a reason to deal with the press in a barbaric way."
In an editorial on its website, the Standard said it had been strengthened by an "incredible outpouring of support".
It rejected allegations by the police that its journalists took money to write certain stories, and in turn accused the government of a "dangerous intolerance".
Demonstrators joined opposition MPs in marching from parliament to the Standard's offices in protest on Thursday.
A group of 27 diplomats called on the Kenyan government to take action against those responsible.
"These acts of thuggery have no place in an open democratic society," said a statement from the US embassy.
The Standard - Kenya's oldest newspaper - has been critical of President Mwai Kibaki's handling of recent corruption scandals.
The government has repeatedly accused the newspaper of fabricating stories.
Three Standard journalists, arrested before the raids over a story about President Kibaki, have been charged with publishing alarming statements and released on bail.