Fijian Prime Minister Frank Bainimarama has expressed his alarm to Scott Morrison about Qantas' bid to increase the number of direct flights to Fiji, hard on the heels of the Pacific Island's national flag carrier warning it would hurt its economy.

Mr Bainimarama raised Qantas' move during bilateral talks in Canberra on Monday, as he also made a pointed reference to differences between the two countries taking some effort to resolve following last month's fiery Pacific Islands Forum meeting, where Mr Morrison was left isolated on climate change.