The Tonga Defence Services say the Kele'a newspaper had been operating illegally and without a proper licence when troops forced its closure on Sunday.
The office of the pro-democracy publication was shut while staff worked towards its weekly deadline.
The editor of the Kele'a, Tavake Fusimalohi, says his newspaper was targetted for exposing government corruption.
But the TDS says they acted because the Kele'a employees were working on a Sunday inside an area of Nuku'alofa restricted because of the current State of Emergency.
A spokesman for the TDS, Solomon Sevelio, says the Kele'a office had moved premises recently and staff weren't caught until last Sunday.
"This is a new building where they moved (to) from their original office and they were in a position of transition. So we could not confirm if they have actually established themselves or not. But we confirmed that last Sunday they actually had their office there. So we cannot enforce others outside this proclamation area if we don't catch them working on Sunday."
Solomon Sevelio says the state of emergency is to expire on Friday.