The Philippines told its fishermen Wednesday to steer clear of a fishing ground in the disputed South China Sea to avoid harassment from Chinese authorities.

The warning came despite a recent ruling by a UN-backed tribunal in favour of the Philippines, as it dismissed China's territorial claims to large swathes of the waters.

Beijing angrily rejected the court's judgement and on Tuesday it announced penalties for "illegal" fishing in its waters including the disputed areas.

"We are aware that China is occupying Scarborough Shoal, so let us wait for clarity on how our fishermen can return there without being subjected to harassment anymore," Manila's foreign affairs spokesman Charles Jose told reporters.

Jose said that while the tribunal ruling was clear, the "reality on the ground" was different.

"The reality is that China is there so we must discuss this," he said.

Asked if this meant Filipino fishermen should avoid the shoal for now, Jose said: "This is for the safety of everyone."

Manila's position is likely to anger critics of President Rodrigo Duterte's new government, which has been accused of taking a soft line with Beijing.

The question of who has the right to fish in the disputed South China Sea has been a major bone of contention between Beijing and Manila, which brought the case to the Permanent Court of Arbitration in The Hague.

Manila lodged the case under its previous government in 2013, saying that after 17 years of negotiations with Beijing it had exhausted all political and diplomatic avenues to settle the dispute.

Vietnam, Malaysia, Brunei and Taiwan also have claims to the sea, through which over $5 trillion in annual trade passes.

In 2012 China took control of the Scarborough Shoal, 230 kilometres (143 miles) from the main Philippine island of Luzon after a stand-off with the country's navy.

It has since driven away Filipino fishermen attempting to fish in the area, sometimes using water cannons.

Duterte has said he wants to repair relations with China that were battered during the term of his predecessor Benigno Aquino.

Duterte, who assumed the presidency on June 30, said he would send former president Fidel Ramos to Beijing as an envoy to negotiate on the issue.

"This is one of the priority issues that we must take up when we go into direct talks with China," Jose said Wednesday.