The project includes radio communications for disaster-focussed agencies, early warning sirens, loud speakers and remote activated radios.
Improvements to Tonga's AM broadcasting service, and training for the disaster office and met service are also part of the plan.
Tonga's Minister for the Environment Poasi Tei said the help is timely given that Tonga is second most-at-risk country in the world for natural disasters.
He cited Polynesia's 2009 earthquake and tsunami, and last year's Cyclone Gita, as examples of devastating disasters endured by Tonga, saying the Japanese project will help save lives.
Photo file: Caption: The trail of devastation left behind by Cyclone Gita in Tonga