America's Pacific commander held talks with the Philippine military Wednesday on ways to strengthen US capacity in the region to deter conflict and maintain freedom of navigation, a Filipino spokesman said.

Admiral Harry Harris, head of the US Pacific Command, outlined a freshly drafted Pentagon report highlighting issues in the South China Sea, where China is in dispute with the Philippines and other neighbours over islands, reefs and waters, said military spokesman Colonel Restituto Padilla.

"It is part of our interest to keep that freedom of the seas going because a lot of trade goes on in these areas," Padilla said of Harris's meeting with Filipino military chief of staff General Hernando Iriberri.

Harris did not speak to the press after meeting Iriberri and later Philippine President Benigno Aquino.

Japan and the Philippines -- both US military allies -- are engaged in tense maritime disputes with China over islands, reefs and waters in the East China Sea and South China Sea, respectively.

Some of the South China Sea reefs and waters claimed by China are also disputed by Brunei, Malaysia, Taiwan and Vietnam as well as the Philippines.

Since last year China has been building new islands over reefs there that Manila alleges could become military bases, and which the US and Philippines say could eventually restrict free movement of shipping in international waters.

Padilla said the Pentagon report -- entitled "Asia Pacific Maritime Security Strategy" -- highlighted the importance of the region to the security of the US and its regional allies.

"They (Washington) wish to strengthen US military capacity to ensure it can successfully deter conflict and coercion and respond decisively when needed," Padilla said.

There was a "very frank and honest exchange" by Harris and Iriberri over "the challenges that we need to face to ensure that no miscalculation occurs in our part of our seas and in the South China Sea", Padilla added.

The military spokesman said no specific details were discussed on how the US strategy will be put into practice, adding further meetings were expected.

US and Filipino troops and navies have been conducting large-scale annual military exercises focusing mainly on maritime capability.