The 449 schools, including some of the top private schools, were identified by a committee appointed by the Delhi High Court and headed by Justice Anil Dev Singh.
Kejriwal said the committee recommended the schools to refund the extra fees but many didn't.
"As they did not comply, the court asked the Delhi government what is being done. We said that we will implement (the report) and as a last resort we will take over the schools," he added.
"We're not against private schools, there is no witch hunting. We are appealing to these 449 schools to implement the committee's recommendations and give back the extra fees.
"We won't be silent over this robbery by private schools. If they don't listen to our appeal, then the Delhi government will take over them with a heavy heart," he added.
He said that his government found that while one school which was not returning extra fees has Rs 19 crore surplus, another has Rs 5 crore in its kitty.
"Is it justified that they charge from the people and then divert the funds?" Kejriwal said, adding that his government was working to fill the quality gap between government and private schools.
Education Minister and Deputy Chief Minister Manish Sisodia said the committee examined 1,108 private schools and found 544 had hiked fees in the name of implementing the Sixth Pay Commission. Of this, 15 schools had paid back.
"Five other schools have deposited money to the court. Seventeen schools had been issued notice, 13 schools were shut and one school was taken over by the government last year.
"Many of them are giving good quality education and we don't want to take them over. Our request is (they must) pay back the extra fees."
But Sisodia warned that the government would be forced to take over the schools if they do not stick to the committee's report.