"This time, our cover story was on labour - how activities of the Maoists affiliated labour unions have been giving unions a bad name. I think the main reason for the attack was this story," Rameshwor Bohara, a journalist, said.
Political analysts say the Maoists have been using their affiliated trade unions to exert control over industries, and are now trying the same technique with the media.
Some companies have been forcefully shut for months from trade union pressure.
Last month Maoists attacked Himal Media and burnt 5000 copies of one of their magazines. No one has been charged with the attack as yet.
Subina Shrestha, Al Jazeera's correspondent in Kathmandu, said: "Now the Maosits are being more brazen, coming in broad daylight and not only vandalizing property but also physically abusing journalists."
Accusations are flowing from the Maoists opponents: "I will not say that the top leaders have been encouraging them but they have been protected by the top leaders of the Maoist party," Madhav Kumar Nepal, of the Nepal Communist Party-United Marxist Leninist, said.
Concerns are also being voiced about the impunity with which attacks are occurring.
"We've had guarantees from the prime minster that this government would respect freedom of expression and particularly freedom of the media and we'd expect to see that happen," Martin Logan, a spoklesman at the Office of the High Commission of Human Rights, said.
Maoist rebels had fought a decade-long civil war against the monarchy before deposing the monarchy and eventually forming a government.
More than 12,000 people died during the war.