Reports said the U.S. WC-135 Constant Phoenix aircraft was flying in worldwide airspace over the sea, when China's Sukhoi Su-30 fighter jets intercepted it.
Two Chinese pilots intercepted the craft, and Lori Hodge - the air force spokeswoman - said in a statement the planes had been acting in an "unprofessional" manner.
Even though China claims that it respects freedom of navigation in the strategically vital area, it objects to United States military activities, especially the collection of signals intelligence by U.S. craft operating near the coast of its southern island province of Hainan, home to several military installations.
An investigation into the incident has been launched by the us military.
Wednesday's incident was the second between US and Chinese planes this year.
"All the US' claims about alleged "unprofessional" actions of the Chinese pilots are not worth a damn".
China declared an air defense identification zone over a large section of the East China Sea in 2013, a move the U.S. called illegitimate and has refused to recognize.
She noted that the WC-135 was on a routine mission at the time of the alleged intercept and was operating within worldwide airspace, Reuters reported. This incident was interpreted as unsafe and also inadvertent by the Navy. The planes came within 1,000 feet of each other, and the US plane had to alter course to make sure there wasn't a collision.
The four-engine WC-135, dubbed the Constant Phoenix, has been deployed in the past to detect North Korea's nuclear activities. "But as for this question you have raised and are concerned about, we need to understand and check what was the actual situation on the scene", she added.
China claims sovereignty over nearly all of the disputed territory in the South and East China seas, though several other countries in the region have competing claims.
Separately, China and South East Asian countries have agreed a framework for a long-awaited code of conduct for the disputed South China Sea, China's foreign ministry said, without giving details on the content.
"This is escalating the situation and absolutely unacceptable", Defense Minister Tomomi Inada told a news conference on Friday, referring to the incursion and drone flight.
"China is escalating the situation unilaterally, and this is totally unacceptable", Inada said at a press conference. A radiation detection aircraft was dispatched to Japan in early April, and several sorties have since been flown in the region.
The Senkaku/Diaoyu chain lies nearly 1,900 km (1,180 miles) southwest of the Japanese capital Tokyo, west of Japan's Okinawa Island, and northeast of Taiwan.