The decision was taken at a meeting of Delhi Cabinet on Saturday chaired by Chief Minister Arvind Kejriwal.
The government has taken this step after distressed parents recently approached it, complaining of fee hike ranging from 20 to 55 per cent.
"As per the Delhi Cabinet's decision, government will only hire the CAG-empaneled chartered accounts to get accounts of schools running on its land audited.
The Directorate of Education (DoE) had recently warned private schools in the national capital citing rules that schools running on the government land cannot do so without prior sanction from the authorities.
In the past, a delegation of parents had met Kejriwal and Deputy Chief Minister Manish Sisodia and apprised them of "arbitrary" hike in school fees.
Sisodia, who also holds education portfolio, had directed the DoE to take necessary action against the "errant" schools that have not only hiked fees but also "compelled" students to buy books from private publishers.