An eight-member Appellate Division bench headed by Chief Justice SK Sinha gave the order on Monday.
President Abdul Hamid on Sunday decided not to issue a gazette over the matter despite a court order requiring the government to do so.
The bench said the president might have been misled regarding issuance of gazette notification on the rules.
"You (the Attorney General) have wrongly explained the disciplinary and conduct rules to the President," the UNB quoted the chief justice as saying.
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"We have not made any disciplinary and conduct rules for judicial officers and Bangladesh Judicial Service. We have just revised the ones provided by you as those were not consistent with the Masdar Hossain case."
In a landmark verdict in the Masdar Hossain case, the Supreme Court on December 2, 1999, issued a 12-point directive for separating the judiciary from the executive.
It also directed the government to formulate separate disciplinary rules for the lower court judges.
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The judiciary was separated from the executive in November 2007 and the government prepared a draft of the related rules.
However, the Appellate Division made some changes in the draft and sent it back to the Law Ministry for issuing a gazette.
On December 1, the court gave the government seven days to issue the notification.
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As the government missed the deadline, the court summoned two Law Ministry secretaries on December 9 to explain the ministry's position.
But the Law Ministry on Sunday issued a notification saying the president had decided against publishing the gazette.