Police and local leaders found the group congregating at a home of one Janviere Ufitamahoro, 32, who escaped.
The religious service was led by one Violette Niyigena, 25, also arrested.
Worshippers belong to five different churches in Rutsiro, including Catholic, Anglican, Seventh Day Adventist and pentacostal.
Rutsiro Acting District Police Commander (Ag. DPC), Chief Inspector of Police (CIP) Elie Niyongabo and the Vice Mayor for Finance and Economic Development, Innocent Gakuru Munyakazi led the enforcement of the directives.
Munyakazi told the violators that adhering to health measures is currently the only way to fight Covid-19.
"It is shocking and irresponsible for you to hold such gathering of people coming from different places disregarding the government directives, amidst this deadly virus, which is still claiming lives," Munyakazi told the violators.
He advised them to rather go to churches that were allowed to resume services instead of putting their lives at risk of catching the virus.
CIP Niyongabo warned against such practices and thanked members of the public, who continue to report violations.
According to the DPC, all the 52 violators were found congested in the small living room with no face mask.
He told the violators that holding such gatherings undermine the government efforts against the pandemic.
"Such gatherings can be the source for further spread of Covid-19 given that you don’t know your status. One of you could be positive, infect all others and spread the virus in your families and communities. Protect yourselves and your families from the virus by complying with the directives and health guidelines. Fear the virus not the Police," CIP Niyongabo said.
Violators were educated on health measures and fined accordingly by the administrative authority.