Hindus claim that remnants of a structure resembling a temple were found when the mosque was being demolished for renovation in April this year.
As the news spread, locals and other activists gathered at the site on April 21. Police intervened to defuse the situation.
The third additional civil court is hearing the petitions from an activist T A Dhananjaya and five others who have demanded a probe after a structure like a Hindu temple was claimed to have been found inside the mosque.
The advocate for the mosque had argued that the matter comes under the Wakf-related court as the mosque is the property of the Wakf Board. He had sought the dismissal of the petition.
The mosque is situated within Ganjimath gram panchayat limits in Mangaluru taluk of Dakshina Kannada district.