"Thrust was released to transfer the probe onto the pre-landing orbit," Roscosmos said in a statement.
"During the operation, an emergency situation occurred on board the automatic station, which did not allow the carrying out of the manoeuvre within the specified conditions."
The lander, Russia's first such mission in almost 50 years, was successfully placed in the Moon's orbit on Wednesday after being launched from the Vostochny cosmodrome in the country's Far East.
Roscosmos did not say if the incident would delay the landing, due to take place on Monday, north of the Boguslawsky crater on the lunar south pole.
In June, Roscosmos chief Yuri Borisov told President Vladimir Putin that such missions were "risky", with an estimated success probability of around 70 percent.
The probe is expected to stay on the Moon for a year, where it is tasked with collecting samples and analysing soil.
Cameras installed on the lander have already taken distant shots of the Earth and Moon from space.
Russia is seeking to restart and rebuild on the Soviet Union's pioneering space programme as the future of its long-running space cooperation with the West looks in doubt amid the offensive in Ukraine.
Russia said it would go ahead with its own lunar plans, despite the European Space Agency announcing it would not cooperate with Moscow on future missions over its actions in Ukraine.
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