Tensions flare between Australia and Japan over controversial whaling program

Australia's relationship with Japan is officially "strong" despite a disagreement over our Asian neighbour's whaling program, following a lightning trip to Tokyo by Prime Minister Malcolm Turnbull.

However, on tensions in the South China Sea, Japan and Australia walk the same line.

"Actions which disrupt, which create tensions, which raise the risk of conflict, whatever the motives of those responsible will result in loss for everybody," Mr Turnbull said.

China is flexing its muscles in the Sea by building artificial islands, causing tensions with neighbours and the United States.

Beijing was angry after an Australian military aircraft flew near the highly-sensitive area.

Seventy years after the end of World War II, Mr Turnbull and Japan Prime Minister Shinzo Abe agreed to take Australia and Japan one step closer to joint military exercises.

It was Mr Turnbull's first visit to Tokyo as Prime Minister, which has been deemed a success, but there was a major sore point over Japan's resumption of whaling in the Southern Ocean.

"It's a matter of major concern, real heartfelt concern, principled concern to Australians," Mr Turnbull said.

Mr Abe pushed back, condemning violence by anti-whaling protestors.

"No violence can be justified regardless of the reason and I strongly urge that necessary measures be taken," Mr Abe said.