The order for a CBI probe into the matter was given by the single-judge bench of Justice Biswajit Basu, which also directed the central agency to submit a report to the court by April 25.
However, the state government moved the division bench of Justice Harish Tandon and Justice Madhuresh Prasad against the ruling, which on Friday upheld the order passed by Justice Biswajit Basu.
The division bench also directed the CBI to submit a report by April 25.
The state government had expressed doubts over the two anonymous letters that alleged irregularities in the recruitment process of GTA-run schools, based on which the CBI probe was ordered.