RNZ reports he said Nauru is deeply saddened by Ratu Joni's death and the country and region had lost a great statesman.
A statement from the Nauru government said Ratu Joni, who is a former Vice-President of Fiji, died in Suva after a short illness yesterday and he will be buried at his home island of Bau next Friday.
Ratu Joni was appointed as Nauru's top judge in September 2014.
Mr Waqa said Ratu Joni was instrumental in the recent reforms of Nauru's legal system, and had re-established integrity and honour to Nauru's court.