"They were in no doubt that they had violated the law as their action obstructed the work of the authorities," Col Winthai Suwaree, the deputy army spokesman, told FM101 radio station.
"But we did not treat the issue from a legal point of view alone. We looked at it from other perspectives," he added.
Col Winthai told reporters earlier that the army opted to retreat instead of taking action to avoid a confrontation with the People's Radio for Democracy Group, a faction of the United Front for Democracy against Dictatorship.
The group has camped out in front of the NACC office in Muang district, Nonthaburi, to pressure the agency into ousting six out of eight commissioners, saying they are working with no royal endorsement.
The NACC had earlier explained that their position was legitimate.
Group leader Somsak Malaithong said his members planned to raise the protest to another level by blocking all entrances of the office to prevent officials from going inside.
NACC officials were forced to hold meetings at their old head office opposite Government House on Thursday.
The rally coincides with caretaker Prime Minister Yingluck Shinawatra being ordered to defend a case of negligence of duty concerning the rice-pledging scheme on Monday. The NACC has alleged Ms Yingluck, chair of the National Rice Police Committee, did not stop the policy despite warnings of corruption.
The radio group removed a military bunker built in a soi behind the NACC office on Wednesday and met no resistance from soldiers who packed their equipment onto a truck and returned to their unit. The soldiers had been ordered to secure the safety of the NACC's building.
Col Winthai said the unit has had to adjust its security operations, including providing more patrols in the area.
But he warned that the radio group must accept responsibility if violence occurs at the location.