President Fernandez has accused Clarin of biased reporting
More than 200 tax inspectors have searched Argentina's biggest newspaper, which is currently embroiled in a fierce battle with the government.
Officials said the raid on the daily Clarin was "routine", but the newspaper accused the government of harassment.
President Cristina Fernandez is trying to push through media reforms which she says will modernise the industry.
But critics say the president's aim is to weaken the Clarin Group, Argentina's dominant media company.
President Fernandez and her husband, former president Nestor Kirchner, have in the past accused Clarin of biased reporting and described the group as a "monopoly".
Thursday's raid came on the same day Clarin newspaper published a report alleging a government farm trade controls agency granted a 10m peso ($2.6m, £1.6m) subsidy to an agricultural firm without authorisation, local media report.
A tax agency spokesman said the raid on the Buenos Aires offices of the paper was similar to those carried out at other companies and was aimed simply at examining the company's books, Reuters news agency reports.
But Grupo Clarin claimed it was a form of government "harassment" and "intimidation".
"We are truly surprised... these types of inspections have never occurred in all of Clarin's history as a newspaper," Martin Etchevers, a group spokesman, said.
"The illegal use of government organisms to attack our companies is a shameful custom."
The raid also drew criticism from the capital's mayor, Maricio Macri, who said the operation "feeds levels of violence and confrontation", the Buenos Aires Herald reports.
Lawmakers are currently debating the media reform bill, which would replace broadcast regulations that date back to 1980, during the country's military dictatorship.
The new rules would force the biggest media groups to sell some of their assets. Grupo Clarin has TV and radio as well as newspaper interests.
Supporters of the bill say it will increase competition between media providers, thus driving down prices for consumers.
But opponents, including Mr Macri, fear the impetus for the bill springs from a personal grudge between the government and the newspaper group.