Mizzima Media confirmed that it along with four other media companies Myanmar Now, 7 Day, Khit Thit media and Democratic Voice of Burma had their licenses to publish and broadcast news revoked.
The news organization's editor-in chief Swe Win said they had expected the raid to have occurred earlier.
"We are now at a point where continuing to do our jobs means risking being jailed or killed," he said. "What is certain is that we will not stop covering the enormous crimes the regime has been committing throughout the country."
State media The Global New Light of Myanmar reported the Ministry of Information had banned the companies "from publishing or broadcasting with the use of a kind of media or technology" on Monday night, after the military, known as the Tatmadaw, confronted protesters with lethal force, killing at least three people nationwide.
Two protesters were were fatally shot by security forces in northern Myanmar while a third was shot dead in the southern Ayeyarwady region as protesters took to the streets in a countrywide strike, Myanmar Now reported.
More than 60 people have been killed and 1,857 have been arrested, charged or sentenced since the coup, Myanmar's Assistance Association for Political Prisoners said in its daily update.
Human Rights Watch early Tuesday also called for the junta to "promptly and impartially" investigate and hold accountable those responsible for the death of Khin Maung Latt, 58, a local politician in Yangon who died in police custody.
AAPP said Latt was arrested Saturday from his home and was tortured to death in his cell that night.
The next day, his family recovered his body from the hospital, HRW said.
"Myanmar's junta runs the security forces and can quickly find out who killed Khin Maung Latt if they want to," Brad Adams, Asia director at HRS, said in a statement. "If they want to show they believe in the rule of law, all those responsible should be held to account. Sadly, Myanmar's security forces seem intent on using nighttime raids and brutal mistreatment to create fear and break popular resistance to military rule."
Late last week, Tom Andrews, the U.N. special rapporteur on the situation of human rights in Myanmar, called for punitive measures to be imposed against the junta for its escalation in violence against protesters who have taken to the streets since it ousted the civilian-elected government in a coup early last month.
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