The Finnish Defence Forces and the National Bureau of Investigation launched two separate probes into the "leak of classified data" after the article was published in the country's leading newspaper, Helsingin Sanomat, on Saturday.
Finland's President Sauli Niinisto said in a statement that the secret documents "had illegally been handed to the Helsingin Sanomat" which could "cause serious damage" to the nation's security.
Journalist Laura Halminen and her colleague Tuomo Pietilainen revealed wide-ranging powers of the Finnish Defence Forces' intelligence research centre near the central city of Jyvaskyla.
Surrounded by tight security in a secluded area, the centre is primarily responsible for "closely monitoring the movements of Russian armed forces" in the region bordering Saint Petersburg, according to the two journalists.
The secret documents on the centre's activities date back 10 years, according to Helsingin Sanomat chief editor Esa Makinen.
The news article wrote that Finland's military intelligence "has developed secret policies that have never been approved in parliament" because the nation doesn't have a comprehensive legislation on its tasks or powers.
Makinen said "the most important task of the media is to monitor" the authorities, adding intelligence agencies have expanded their operations.
Police on Sunday evening searched Halminen's home, seizing her phone, computer and several USB flash drives, according to the Helsingin Sanomat.
Police searched her home after she initially had tried to smash her computer hard drive with a hammer, which caused smoke, and then called the fire brigade.
"By destroying the device, I wanted to ensure the confidentiality of my sources," Halminen, who has also reported on neo-Nazi movements, told the paper.
The incident has raised alarm among media organisations in the nation which was ranked first in the World Press Freedom Index for the past five years. Finland came in second place after Norway this year.
Riikka Venalainen, editor-in-chief at the Finnish public broadcaster Yle, said the police search at Halminen's home was an incident "we are not used to seeing in Western societies".
"There's a reason to be concerned," she told Yle.
Arno Ahosniemi, head of Finland's association for editors-in-chief, added: "I don't remember this kind of case (having happened) in Finland before."
Finland is to hold presidential elections on January 28.
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