The three were stopped as they travelled back from a drugs-burning ceremony organised by the Ta'ang National Liberation Army (TNLA) in the eastern state of Shan to mark the UN's anti-drug trafficking day.
They included reporters from The Irrawaddy and DVB, two publications that for years challenged the then-junta with their independent reporting from outside the country.
"They are under interrogation," ministry of information spokesman Ye Naing told AFP.
The military said on Monday they were stopped near Phayargyi village in Namhsham township. A TNLA source on Tuesday confirmed they were still being held in the area.
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They may now face charges under the Unlawful Associations Act, a law used by the former military government to silence dissent during its half-century in power.
The legislation, which carries a maximum three-year prison sentence, was regularly used against anyone who made contact with the armed insurgent groups which have been fighting the state for decades.
"Their arrests send a chilling message to Myanmar's already embattled media," said Amnesty International's director for Southeast Asia and the Pacific, James Gomez.
Myanmar Journalists Association called for "prompt measures" to be taken to ensure the three men are freed.
The arrests come amid a groundswell of activism among Myanmar's journalists aimed at quashing a controversial online defamation law which critics say is being used to stifle press freedom.
Pressure has mounted since last month, when the army sued the editor in chief of The Voice and a satirist for uploading a link to an article poking fun at the military's leaders.
Prosections under the law have surged since Aung San Suu Kyi's National League for Democracy came to power last year, with social media satirists, activists and journalists increasingly targeted.
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