The move comes after the magazine published a story on corruption in the elite Russian police circles, reports the online Russian political newspaper Gazeta.ru.
The liberal independent weekly news magazine published the article in February. It featured interviews with current and former officers of the Omon riot police, the Special Purpose Police Unit of Russia.
In the interview, some police personnel accused their superiors of abusing their powers and forcing them to provide protection to businessman, take part in raids over property disputes and supply prostitutes. The elite Omon police are recruited to guard officials, storm hideouts of organised crime gangs and control riots.
The New Times said it would appeal to the court to fight its case. In March, the interior ministry of Russia denied the allegations and said it was the victim of an "information campaign" to discredit it. The ministry has sued the weekly for defamation.