Nileswaram police have arrested the Imam of a mosque and his aide for conducting prayers at the Arai Juma masjid in Madikkee Village, Kasaragod District.
More than 25 people attended the prayers amid state lockdown.
Kasaragod District Collector, D Sajith Babu, has ordered for a case to be filed against them under section 269 of IPC.
The collector also directed the police to register a case against the mosque committee chairman and secretary for violating the lockdown guidelines.
This comes at a time when Kasaragod has been declared a COVID-hotspot, with the highest number of positive cases reported in Kerala.
The district administration had issued strict guidelines to avoid all public gatherings and religious ceremonies.
Earlier on Friday, nine more people tested positive for the novel coronavirus in the state increasing the state tally of positive cases to 295.
The total number of Covid-19 positive cases in India climbed to 2902 on Saturday, according to Ministry of Health and Family Welfare. This includes 2650 active cases with 183 patients cured or discharged.