The fishermen allege that China, which has controlled the Scarborough Shoal since a brief 2012 stand-off with the Philippines, is violating their rights to food and livelihood by driving them away, lawyer Harry Roque told AFP.
Signed by 30 fishermen, the petition was sent via email to the UN High Commissioner for Human Rights and others in the organisation in Geneva yesterday, he said.
"They are asking for a remedy. (What they want is) no one telling them where and when they can fish," Roque said.
The shoal lies 220 kilometres off the main Philippine island of Luzon and 650 kilometres from Hainan island, the nearest major Chinese land mass.
The Philippines claims the shoal is within its 200-nautical mile exclusive economic zone.
The government has lodged a separate appeal before a United Nations arbitration tribunal to declare China's sovereignty claim over most of the South China Sea as illegal.
In their petition, the Filipino fishermen cited another supposed incident in April last year when Chinese authorities on speedboats and armed with assault rifles allegedly drove them away, shouting: "Go away, go away, three miles, China island," the 22-page "urgent appeal" read.
The 30 fishermen asked the United Nations to "remind, declare, and direct China and its state agents to cease and desist from violating (their) human rights-including the right to livelihood, the right to adequate food, and the right life".
A recent poll showed eight in 10 Filipinos fear the festering sea dispute with China might lead to "armed conflict" with their powerful Asian neighbour.
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