The remains, the NGO quoted local residents as saying, were suspected to be those of Bundu Dia Kongo sect followers because shreds of cloth and flags used by its members were found at the site.
Gonde denounced a continuing crackdown on the sect, saying security personnel were trying to apprehend some followers who had escaped into nearby forests.
Scores of people were killed in February and March during clashes between police and followers of Bundu Dia Kongo, which is contesting state authority. Aid workers said many others were wounded - some of whom sought treatment at various health facilities.
Aid workers said they saw empty villages with razed homes and that some of the wounded were forced to flee health centres. Some of the victims of violence were hit by stray bullets when they fled.
Bundu Dia Kongo’s spiritual leader and national assembly deputy, Ne Mwanda Nsemi, said he would initiate international judicial proceedings against “the massacre” of his members.
The sect is seeking to emancipate traditional African or Congolese culture and demands the restoration of the former Kingdom of the Congo. It has set up tribunals to try citizens who break the law and has its own police force. Occasionally they lower the national flag to hoist their own.