The abnormality occurred due to "complicated lunar surface environment," the State Administration of Science, Technology and Industry for National Defence (SASTIND) said on Saturday, without giving further details.
The abnormality emerged before the rover entered its second dormancy at dawn on Saturday as the lunar night fell, according to SASTIND.
The lander, another part of the Chang'e-3 probe, also "fell asleep" earlier on Friday.
The pair went dormant for two weeks about one month ago when the first lunar night of the mission occurred.
One night on the Moon is about 14 days on Earth, during which the temperature falls below minus 180 Celsius. During the lunar night, there is no sunlight to provide power to Yutu's solar panel.
After the first dormancy, the lander's Moon-based optical telescope carried out observation of the sky, while its extreme ultraviolet camera observed the plasmasphere over the Earth, according to SASTIND.
The lunar probe mission, comprising the lander Chang'e-3 and rover Yutu, was launched in December as part of the second phase of the Chinese Lunar Exploration Programme.
The mission, which made the first soft-landing on the Moon since 1976, makes China the third country to successfully send a lunar rover to the moon, after the US and the former Soviet Union.