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 yesterday 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.
"The reality is that China is there so we must discuss this," he said.
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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.
Vietnam, Malaysia, Brunei and Taiwan also have claims to the sea, through which over USD 5 trillion in annual trade passes.
In 2012 China took control of the Scarborough Shoal, 230 kilometres 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.
"This is one of the priority issues that we must take up when we go into direct talks with China," Jose said today.