The information - from fishermen who have just returned from the shoal - came despite earlier Philippine government statements that the Chinese had left the outcrop they seized in 2012.
A spokesman for President Rodrigo Duterte had said today there were no longer signs of Chinese ships at the shoal, after Duterte visited China to repair frayed ties.
However Defence Department spokesman Arsenio Andolong said the fishermen who visited the shoal yesterday still saw Chinese coastguard ships there.
China took control of Scarborough Shoal, 230 kilometres (140 miles) west of the main Philippine island of Luzon, in 2012. It drove Filipino fishermen away from the rich fishing ground, sometimes using water cannons.
In a case brought by then-president Benigno Aquino, the Philippines won a resounding victory over China at an international tribunal earlier this year.
However Aquino's successor Duterte played down this victory in a visit to China earlier this month, putting territorial disputes on the back-burner and focusing instead on Chinese aid.
Chinese President Xi Jinping told Duterte there was no reason for hostility and difficult topics "could be shelved temporarily".
The Chinese occupation of the shoal has been a sore point in relations, with Filipino fishermen frequently complaining that Chinese ships drive them away from their fishing grounds.
Newspaper reports today also said fishermen from the northern province of Pangasinan were able to fish at Scarborough Shoal, with the Chinese watching but not interfering.
"Happy days are here again," the Philippine Star quoted one fisherman as saying.
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