The Thai Journalists Association, which comprises representatives from the kingdom's newspapers, raised concerns on Saturday after around 30 troops held a two-day protest calling for an apology.
"The TJA calls for the army to stop interfering in the media in any way. If the media cannot work independently, the public will not get complete information and facts," it said in a statement that also called on the media to avoid bias.
Thailand's military, which has a long history of intervening in politics, including a string of coups, said it had instructed the soldiers involved to end their protest.
"The army chief said... 'We have to forgive, not create more conflict'," army spokesman Colonel Sansern Kaewkamnerd told AFP.
But he rejected claims of media interference.
"They didn't do anything except express their opinions. They did not hurt anybody or close the entrance of the headquarters," the spokesman said.
The rally was against the normally pro-military Asia Satellite TV station, owned by the founder of arch nationalist "Yellow Shirt" movement Sondhi Limthongkul.
Groups aligned to the Yellows -- arch rivals of the "Red Shirts" and ousted premier Thaksin Shinawatra, whose sister Yingluck is the country's current Prime Minister -- have made repeated calls for the army to flex its muscles more strongly.
Thailand has been deeply divided since a 2006 coup by royalist generals toppled Thaksin from power, with rivalry between the Yellows and the mainly rural working class Reds spilling into occasional bloodshed.
Army chief Prayuth Chan-O-Cha is reported to have overseen the military crackdown on a rally by the Red Shirts in the heart of Bangkok in April and May 2010 that left more than 90 people dead.
But he has since shown willingness to work with Yingluck's Red-backed government.
Rights groups say media freedom has been among the victims of the country's political divisions, with thousands of webpages closed by successive governments and strict royal insult laws that activists believe have been used to stifle dissent.