Metropolitan Magistrate Abhilash Malhotra gave the order after observing there is a delay in filing the action-taken report that had stalled the hearing on the complaint.
The court said the matter was first probed by the IP Estate police but transferred to the Economic Offence Wing, before it was handed over to the ACB.
"It is clear that due to the Delhi Police indecisiveness on the choice of investigating agency, the filing of the action-taken report has been delayed," the court said.
The court directed senior police officials to ensure that no further delay is caused in filing of the report.
Earlier, the investigating officer in the case sought three more weeks to file the report, contending he had received the file only on Tuesday from the earlier probe agency.
The court is hearing a criminal complaint filed by Roads Anti-Corruption Organisation founder Rahul Sharma and its Secretary Viplav Awasthy, who sought registration of a case against Mr Kejriwal, his brother-in-law Surender Kumar Bansal, and a Public Works Department officer on charges of cheating, forgery and criminal conspiracy.
The complainants accused them of cheating and defrauding the treasury to the tune of over Rs 10 crore.