The substances were in 22 drums.
The operation was conducted jointly by Ndera Police Station, Rwanda Standards Board (RSB) and local authorities.
The distillery located in Cyaruzinge cell produces illicit brew called Agasusurutso. The owner is still on the run.
Olivier Mwizerwa from RSB said the distiller was counterfeiting Agasusurutso, which is normally produced by a licensed dealer.
The counterfeiter, Mwizerwa said, was using ginger, sugar, spirit and water, among others, which are harmful for human consumption.
"The colour, alcoholic content and smell change when you mix these raw materials and have ill-effects on consumers. This is against the recommended standards," Mwizerwa said.
"It has been established that when you consume such concocted products, you are likely to go blind especially because of the added spirit.
The packaging itself can be dangerous. They were packaging it in plastic bottles and the raw materials they use can not be mixed with plastic products because it can be the source of cancer," he added.
RSB specifies that “only food grade processing aids recognized as safe for human consumption shall be used during the manufacture.”
Other standard requirements include labeling as a prerequisite; the name of the products, physical and postal address of manufacturer; net contents in milliliters or liters; ethyl alcohol content; date of manufacture and expiry date; storage instruction; statutory warnings; and list of ingredients in descending order.
Angelique Uwinkindi, the acting executive secretary for Ndera said the district had warned the producer against the illegal acts but he switched to operating in the night.
She added that there were reports of violence in families and communities in Ndera caused by abuse of these illicit drinks.
Jean de Dieu Twagirimukiza, a local resident collaborated Uwinkindi’s message saying that he lost control and battered her wife after consuming the illicit brew, which prompted his spouse to leave him.
Chief Inspector of Police (CIP) Marie-Gorette Umutesi, the Police spokesperson for City of Kigali said the operations against illegal distilleries and dealers have been going on for a while and scores have also been arrested in Nyarugenge and Kicukiro in connection with the act.
"We are working with the local communities, RSB and local leaders to identify and arrest distillers and sellers of these illicit drinks," said CIP Umutesi.
She added that Police and RSB first intercepted a consignment of the illicit drink in Nyarugenge market and they traced the source to the distiller in Ndera.
Anyone convicted as a "major dealer" in narcotic and psychotropic substances faces between seven years and life imprisonment.
All drinks with alcoholic content above 45 percent or with unknown alcoholic content is considered as a psychotropic substance.