Tonga's Prime Minister has ordered an investigation into over 600-thousand US dollars worth of missing money that was meant to go towards cyclone recovery.

Photo: Scott McLennan

The Ha'apai group was hit hard by Cyclone Ian in 2014, killing one, injuring dozens and leaving thousands homeless.

The reconstruction effort has been beset by delays, miscommunication, quality concerns and land issues, with 75 homes still needing to be rebuilt.

Ha'apai Governor Mo'ale Finau said he welcomes the investigation as he had heard rumours of funds being misappropriated in the past.

Mr Finau said two government ministries in particular needed to provide information.

"The project is been under the control of the Ministry of Infrastructure but there has been a committee, under the Deputy Prime Minister, he has a ministry called MEIDECC for disasters. So I can say that ministry and the Ministry of Infrastructure, they are the ones that should come up now with an answer for that issue."