The Tonga Defence Services, TDS, say the Kele'a newspaper was closed on Sunday because it was operating without a license.
The office of the pro-democracy paper was forced to close by troops as it worked towards its weekly deadline.
The editor of the Kele'a, Tavake Fusimalohi, says it was targetted for exposing government corruption.
But the military says it closed Kele'a for working on a Sunday inside the area of Nuku'alofa restricted under the current State of Emergency.
A spokesman for the TDS, Solomon Sevelio, says the military noticed an increase in foot traffic in and out of the Kele'a office.
"I'm not so sure whether they were working on the last couple of Sundays in small numbers and whether they should be working or not because they don't have a license to work on Sundays regardless. But then last Sunday there were more than five people working there so it was kind of standing out to everybody to see that they were actually operating on Sunday."
Solomon Sevelio of the TDS.