Mr. Duterte’s most recent trip to China, in the spring, was his fourth since becoming president, and he returned yet again with billions of dollars’ worth of pledges from Chinese businessmen.

But the sinking of the Filipino boat, FB Gimber1, which came after a swarm of hundreds of Chinese vessels blocked Filipino fishermen from reaching their traditional fishing grounds earlier this year, has thrown bilateral relations off balance.

Filipino politicians on both sides of the aisle were demanding answers from China. It was not clear whether the sinking, if not accidental, was in any way directed by Beijing or simply a rogue act.

“Even if this is a Chinese fishing boat, I think this is just an incident among the people, not related to governments,” said Hu Bo, an associate researcher at the Institute of Ocean Research at Peking University in Beijing.

In years past, Chinese fishing boats have launched assertive forays into disputed waters, with white hulls, as Coast Guard ships are known, keeping a discreet distance.

But in some cases, the Chinese Coast Guard has intervened directly, such as in 2016, when it forced the breaking of the tow line of an Indonesian maritime task force vessel, which had been hauling in a Chinese fishing boat operating well within Indonesia’s exclusive economic zone.

On Wednesday, Defense Secretary Delfin Lorenzana of the Philippines said the Chinese boat had intentionally rammed the FB Gimber1 as it was anchored near Reed Bank, known in the Philippines as Recto Bank, a disputed area where the two countries have discussed jointly exploring for oil and gas.