President Rodrigo Duterte is planning to raise the Philippine flag on the second largest island in the disputed waters of the South China Sea which his country occupies, a plan unlikely to sit well with Beijing.

He has also ordered his military to fortify the nine islands and reefs the Philippines has claimed in the Spratlys chain in the southern half of the South China Sea.

"It looks like everyone's trying to grab islands. Let's claim what's ours now and make a strong point there that these are ours," Mr Duterte told reporters yesterday at a military base on Palawan Island.

"There are so many islands, I think nine or 10. Let us put structures and the Philippine flag there," he said, referring to his country's claims.

Mr Duterte said he might fly to Thitu Island on June 12 and personally raise the Philippine flag there to mark 119 years of independence.

No bigger than 37ha, Thitu lies 480km west of Palawan and just 24km from Subi Reef, which China has transformed into an island large enough to accomodate a 3km airstrip, radars and anti-air weapons systems.

There are about 100 settlers and a contingent of marines on Thitu. Mr Duterte wants more barracks to be constructed on top of plans announced earlier to build a new port, repave an airstrip and repair existing structures there.

The Philippines has eight other outposts in the Spratlys, but these consist of scrappy groups of a few men and some wood and iron meant to discourage interlopers.

One is a derelict transport ship the Philippine Navy ran aground in 1999 on Second Thomas Shoal to prevent China from moving on it. The shoal lies 34km from another Chinese man-made island, Mischief Reef.

In a statement, the Philippine Defence Department said Mr Duterte now wants to build barracks, water treatment and sewage systems, lighthouses and shelters for fishermen in these outposts.

Mr Duterte appears to be altering his tone with regard to the claims in the disputed waters. Since he took office last year, he has gone to great lengths to rebuild ties with Beijing, strained by a case Manila filed challenging China's claims to nearly all of the South China Sea.

The Philippines won that case, but Mr Duterte instead chose to set aside the victory as he sought billions in investments and grants from China.

In a separate development yesterday, Chinese coastguard vessels were reported to be maintaining a near-constant presence around reefs claimed by Malaysia.

Citing ship-tracking data provided by the Asia Maritime Transparency Initiative, The Guardian newspaper said that three Chinese ships patrolled the Luconia Shoals, an area of islets and reefs that are more than 1,600km from mainland China and about only 145km north of Borneo, in January and February.

The United States-based group said the two-month deployment was not unusual and was consistent with regular rotations of up to 11 Chinese patrol ships it had traced in the area since late 2015.

Control over the South China Sea, a route for half of the world's commercial shipping, has become a major international conflict point, with Beijing asserting sovereignty over maritime areas also claimed by Vietnam, Taiwan, Malaysia, Brunei and the Philippines.