The Philippines and Australia have discussed pursuing joint patrols in the South China Sea, days after the South-East Asian country held similar talks with the United States on the need to counter China's assertiveness in the strategic waterway.

Australian Defence Minister Richard Marles met on Wednesday with Philippine counterpart Carlito Galvez in Manila, something they said they plan to do yearly to deepen their security ties.

"We did talk today about the possibility of exploring joint patrols and we will continue that work and we hope that comes to fruition soon," Mr Marles said at a joint news conference.

"As countries which are committed to the global rules-based order, it is natural that we should think about ways in which we can cooperate in this respect."

With some overlapping maritime claims, the Philippines is ramping up its attempts to counter what it describes as China's "aggressive activities" in the South China Sea, which has also become a flashpoint for Chinese and US tensions around naval operation.

On Tuesday, a Philippine Coast Guard (PCG) aircraft flew over the South China Sea, as part of efforts to boost its presence in contested waters and protect what it says is its maritime territory.

In a statement, the PCG said it saw a Chinese coast guard vessel and dozens of what it suspected were boats manned by Chinese militia around the Second Thomas and Sabina Shoals, both of which are inside the Philippines' exclusive economic zone.

The PCG ordered the suspected militia to leave, telling them "they were not authorised to loiter nor swarm these shoals".

China's embassy in Manila did not immediately respond to a request for comment.

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