China says the Philippines ignored proposals it put forward to "manage" their dispute in the South China Sea.
An unnamed senior Chinese official told news outlet the Manila Times that the deal was "met with inaction by the Marcos administration".
President Ferdinand Marcos Jr said they did not reject the deal, but said it stood on a "questionable" premise.
The South China Sea is at the centre of a territorial dispute between China, the Philippines and other countries.
But tensions between Manila and Beijing have sharply escalated in recent months. At the heart of it is a decaying ship on Second Thomas Shoal that the Philippines have purposely marooned to reinforce its claim in the shoal.
Routine missions to bring food and essentials to a handful of Filipino soldiers on the ship named Sierra Madre has resulted in encounters between the Philippine Coast Guard escorts and the China Coast Guard.
The Manila Times, quoting an unnamed senior Chinese official, had reported on Monday that China offered a proposal last April but was "met with inaction by the Marcos administration".
The report said China's proposal included allowing Filipino resupply missions to the Second Thomas Shoal, as long as it involves just one ship and that it does not deliver large-scale building materials.
This was based on an "understanding" between China and Mr Marcos' predecessor, Rodrigo Duterte, claimed the report.
On Tuesday, the Philippines' Department of Foreign Affairs (DFA) responded to the report, denying the allegations. They said that while some of China's proposals were "workable", others were "contrary to our national interests".
China had responded to the Philippines' counter-proposals with another set of counter-offers, the DFA added.
Mr Marcos later clarified that China's proposals stood on a "questionable premise", referencing China's so called 10-dash line map.
"We have not rejected any proposals that China has made to us but the premise is something that we questioned... that premise that China has made is that their territory follows what is now described as a 10 dash line," he said in Germany, where he is on an official visit.
He added that China's claims in the South China Sea were "not recognised by any country... certainly not by the Philippines".
China claims by far the largest portion of territory in an area demarcated by the "10-dash line". The line comprises ten dashes which extends hundreds of miles south and east from its most southerly province of Hainan.
Mr Marcos assumed the presidency in June 2022 and pivoted the Philippines back to its traditional ally, the US, drawing China's ire.
After the first collision between Philippine and Chinese ships last October, US President Joe Biden said Washington would defend Manila if Beijing attacks. The two countries are bound by a mutual defence treaty.
Mr Duterte, on the other hand, had pursued stronger economic and political ties with China. He scaled back military co-operation between the Philippine and US militaries and refused to flout an international arbitration court ruling that rejected China's vast sea claims that also overlap with those of Vietnam, Malaysia, and Brunei.
