Manila-based Social Weather Stations said this sentiment had weighed on people's minds since the Philippines backed down from a tense standoff with China over control of rich fishing grounds around Scarborough Shoal in 2012.
The study showed 84 per cent of 1,200 respondents were "worried" about armed conflict with China.
About half were "worried a great deal" while more than a third were "somewhat worried".
The same poll has been conducted every year since 2012, and in each of the surveys at least 80 per cent of respondents have been concerned that the sea dispute could escalate into a full-blown conflict with the Philippines' powerful Asian neighbour.
"This is precisely why our government has pursued peaceful means to resolving the dispute."
The Scarborough Shoal standoff ended with Beijing taking control of the fishing area, which lies 220 kilometres (140 miles) off the main Philippine island of Luzon.
The shoal lies 650 kilometres from Hainan island, the nearest major Chinese land mass.
China and the Philippines are also in dispute over other islands and reefs in the South China Sea, with the Philippines seeking arbitration from a United Nations-backed body.
Vietnam, Malaysia, Brunei and Taiwan also have overlapping claims over the South China Sea, which hosts major shipping lanes and is believed to hold vast mineral reserves.
China has ramped up construction of artificial islands in the area to reinforce its sovereignty claim over most of the sea, even waters close to the shores of its neighbours.
The Philippine poll also showed a rising number of Filipinos disapproved of their government's handling of the dispute as China undertook other actions to reinforce its claim, including alleged harassment of Filipino fishermen.
Forty-six per cent of respondents disapproved of their government's response to the Chinese actions at the shoal, higher than 32 percent last year and 27 percent in 2013.
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