A warning has been issued to Beijing that a surge in territorial "incursions" by Chinese vessels in the South China Sea "may trigger unwanted hostilities that both countries would rather not pursue", reported Reuters.
The prolonged presence of the boats in the Philippines' Exclusive Economic Zone (EEZ) was fraught with potential to strain bilateral relations, according to Salvador Panelo, Chief Presidential Legal Counsel of Philippine President Rodrigo Duterte.
"We can negotiate on matters of mutual concern and benefit, but make no mistake about it - our sovereignty is non-negotiable", said the presidential legal counsel in a statement.
Earlier in March, Manila lodged a diplomatic protest over the presence of Chinese boats inside its 200-mile exclusive economic zone at Whitsun Reef in the South China Sea as "swarming and threatening", insisting that the vessels were manned by Beijing's maritime militia.
"The Philippines calls on China to immediately withdraw these vessels flying its flag. Neither the Philippines nor the international community will ever accept China's assertion of its so-called 'indisputable integrated sovereignty' over almost all of the South China Sea", the National Task Force for the West Philippine Sea said in a statement.
The Philippines subsequently spotted unknown structures installed on a series of reefs where the "flotilla" of Chinese fishing vessels was earlier tracked.
"The Laws of the Sea gives the Philippines indisputable and exclusive rights over the area. These constructions and other activities, economic or otherwise, are prejudicial to the peace, good order, and security of our territorial waters. These structures are illegal", Lt. Gen. Cirilito Sobejana, Chairman of the Joint Chiefs of Armed Forces of the Philippines, pointed out in a statement.
Chinese diplomats dismissed the claims, saying the boats were sheltering from rough seas and there were no militia aboard.
The Whitsun Reef is part of the Spratly archipelago - a resource-rich chain of islands, islets, and atolls - claimed by Brunei, China, Malaysia, the Philippines, Taiwan, and Vietnam.
The Philippines maintains that the reef falls inside the country's exclusive economic zone.
China's territorial claim to the "nine-dash line" covering most of the South China Sea was dismissed by a 2016 United Nations tribunal ruling. The arbitration had been initiated by Manila in 2013.
Beijing has refused to recognise the decision of the Hague-based Permanent Court of Arbitration, which it called "a sham".
The US has also been actively weighing in on the South China Sea-related dispute, despite Washington having no claims to the area. The US Navy has repeatedly sent its ships to the South China Sea on so-called "freedom of navigation" missions that have triggered harsh criticism from Beijing, who slammed them as acts of "provocation".