The schools have urged PM Modi to look into the allegations and launch an investigation.
Two associations representing at least 13,000 schools in Karnataka have written to Prime Minister Narendra Modi, accusing the Basavaraj Bommai-led BJP government of corruption.
The Associated Managements Of Primary And Secondary Schools and The Registered Unaided Private Schools Management Association have urged PM Modi to look into alleged bribes that are being demanded by the state education department to issue recognition certificates to educational institutions.
"Unscientific, irrational, discriminatory and noncompliance norms are applied to only unaided private schools and huge corruption is in place," the letter read.
The associations claimed that multiple complaints and pleas to state education minister BC Nagesh have gone unattended, and demanded Mr Nagesh's resignation.
"The education ministry is impatient to listen and understand the actual pathetic situation of the whole system and resolve the issues. Two different BJP ministers literally caused lots of damage to budget schools rather than those schools that are commercialising education by allowing more and more investors to set up, directly costing more fees per child for parents," the letter added.
The associations also alleged that government-prescribed textbooks have still not reached the schools despite the beginning of the new academic year.
"The education minister has no concern to liberalise the rigid norms and frame rules and regulation that both public and private schools can practically and physically implement without burdening parents and students," read the complaint.
The school associations have urged PM Modi to look into the allegations and launch an investigation into the affairs of the Karnataka education ministry.