The Philippines has claimed that China has deployed almost 100 vessels in a disputed area of the South China Sea, raising fresh concerns about tensions in the region.

China denies it has increased its presence in the waters around the Scarborough shoal. The countries are in talks to defuse the two-month standoff.

The South China Sea has seen growing friction between China and its neighbours in recent years, with experts blaming valuable natural resources and the depletion of fisheries as well as long-term sovereignty disputes. They fear it is becoming harder to contain the conflict, which has also become conflated with Sino-US competition in south-east Asia.

Manila's foreign affairs spokesman, Raul Hernandez, said there were 96 Chinese vessels at the shoal on Tuesday, including four government ships as well as fishing boats and dinghies, while the Philippines had only two vessels in the area.

He added that despite a seasonal fishing ban imposed by both countries, Chinese ships had been seen fishing and collecting protected corals. "It is regrettable that these actions occurred at a time when China has been articulating for a de-escalation of tensions and while the two sides have been discussing how to defuse the situation in the area," Hernandez added.

On Monday Manila handed the Chinese ambassador a note protesting at the presence of 77 vessels, demanding their immediate withdrawal, he added.

But China's foreign ministry spokesman, Hong Lei, said only around 20 fishing vessels were working in waters near the shoal, a similar number as previous years. "Their fishing activities are in line with Chinese law and the fishing ban," he told a daily news briefing. "The Filipino side recently carried out some provocations in the area and China took actions in response."

Stephanie Kleine-Ahbrandt, North Asia director for the International Crisis group, said it had appeared the current crisis was easing. "The mutual fishing bans were promising ... the bananas are flowing again," she said.

This month China impounded banana imports from the Philippines, saying stricter checks were necessary. Kleine-Ahbrandt said: "The skirmishes that have taken place there are getting harder and harder to de-escalate because of the factors such as military build-up in the region. We see this as turning into a spiralling security dilemma."

She said internal jostling for power in China appeared to have contributed to the latest tensions, but added: "China is not alone at all in raising the stakes in the South China Sea. Vietnam and the Philippines continue to have worrying risk factors, including nationalist sentiment but also their economic situations."

There was a danger of Beijing and Manila encouraging nationalist sentiment to justify their sovereignty claims, but then finding it harder to back down as a result, she added.

Tensions had cooled in the region after a period of antagonism over the complex territorial dispute – which involves six countries – led to a diplomatic charm offensive by China.

But they flared again in April, when the Philippines sent a warship to the area and said it had found Chinese fishing vessels there with illegal coral and fish.

Speaking before the latest Filipino claims, Dong Manyuan, deputy director of China Institute of international studies, said the Philippines had used the issue to distract attention from domestic problems.

"The government incited local people's patriotic emotions to meet the desires of few politicians," he told the Guardian. But he said it had miscalculated, overestimating US willingness to get involved and underestimating China's determination to defend its sovereignty.