The Philippines will keep asserting its rights in the South China Sea after it reached a "provisional arrangement" with China about its resupply missions to the contested Second Thomas Shoal, the foreign ministry said on Monday.

While neither the Chinese foreign ministry nor the Philippines' Department of Foreign Affairs (DFA) provided details of the arrangement, Manila said it "will not prejudice our respective national positions".

"In our desire to de-escalate the situation in the South China Sea to manage differences in a peaceful manner, we emphasize that the agreement was done in good faith and the Philippines remains ready to implement it," the DFA said in a statement.

"We urge China to do the same."

The Chinese foreign ministry confirmed the "temporary arrangement" with the two sides agreeing to jointly manage maritime differences and de-escalate the situation.

China claims nearly all of the South China Sea, including the Second Thomas Shoal, where the Philippines maintains a rusty naval ship, the Sierra Madre, that it deliberately grounded in 1999 to reinforce its maritime claims.

Manila regularly sends supply missions to sailors stationed at the shoal, turning it into a flashpoint with Beijing.

The Chinese foreign ministry reiterated its demand for the Philippines to tow away the grounded warship and said it would not accept Manila shipping large amounts of building materials to the shoal.

"Between now and when the warship is towed away, should the Philippines need to send living necessities to the personnel living on the warship, China is willing to allow it in a humanitarian spirit if the Philippines informs China in advance and after on-site verification is conducted," it said in a statement.

The Philippine has previously said it was against informing China in advance about its resupply missions, which it maintains are lawful, and said this had not changed under the new deal despite the statement from the Chinese ministry.

"The principles and approaches laid out in the agreement were reached through a series of careful and meticulous consultations between both sides that paved the way for a convergence of ideas without compromising national positions," the Philippines' DFA said.

"The spokesperson's statement therefore regarding prior notification and on-site confirmation is inaccurate," it added.

China rejects a 2016 ruling by the Permanent Court of Arbitration in the Hague that Beijing's expansive claims had no basis under international law. The case was brought to the court by the Philippines.

(Reuters)

An aerial view shows the BRP Sierra Madre on the contested Second Thomas Shoal, locally known as Ayungin, in the South China Sea. (Reuters)

Philippines says to still assert South China Sea rights after resupply deal with China