JAKARTA, Indonesia — Indonesia is holding the crew of a Chinese fishing boat it says was fishing illegally last week in the South China Sea, an official confirmed on Monday. It was the third maritime skirmish — all involving warning shots — between the two countries in the past three months.

The latest episode occurred on Friday when Indonesian warships challenged a group of Chinese fishing boats operating within Indonesia’s 200-mile exclusive economic zone off the Natuna Islands, northwest of Borneo, said Atmadji Sumarkidjo, a spokesman for Indonesia’s Coordinating Ministry for Political, Legal and Security Affairs.

The Indonesian Navy fired warning shots to get the fishing boats to halt, which the Chinese say injured one sailor, and confiscated one boat and detained its seven-member crew, Mr. Atmadji said. The crew was taken to the Natuna Islands, he said. The injured person was not one of those detained and was treated on the Chinese island of Hainan.

“Like the previous incidents, the Chinese ships were fishing in the area that we claim is part of our E.E.Z.,” Mr. Atmadji said, referring to the exclusive economic zone. “The navy pursued them, and they tried to run away and did not obey our instructions to stop.”

Hua Chunying, a spokeswoman for the Chinese Ministry of Foreign Affairs, issued a statement on the ministry’s website on Sunday contending that the fishing boats were operating in “China’s traditional fishing grounds” in the South China Sea. The statement said that the boats were “harassed and shot by several Indonesian naval vessels.”