A bench of Justices G S Sistani and Sangita Dhingra Sehgal said Prakash was the chief secretary and asked how things would work if he was not respected.
"Efforts should have been made to assuage tempers on both the sides. Such notices add fuel to the fire," the bench observed.
"He is your chief secretary. If you do not respect him then how will things work. Was there no other way of calling him? it asked.
The court was hearing the chief secretary's plea challenging a breach of privilege notice issued to him by Delhi Assembly privilege committee for allegedly skipping a meeting called by the panel.
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During the hearing, which remained inconclusive and will continue after lunch, the high court said the matter should have come up before a single judge bench.
Appearing for the chief secretary, senior advocate Siddharth Luthra said, "When people like Amanatullah Khan are in the committee, what purpose will be served by attending such meetings."
Earlier in the day, a bench of Acting Chief Justice Gita Mittal and Justice C Hari Shankar agreed to hear the matter and directed that it be listed it before appropriate bench.
The chief secretary's counsel submitted that the bureaucrat was summoned to appear before the privilege committee for inquiry without being provided any copy of the complaint or opportunity to respond to the same.
The panel had on February 21 recommended privilege proceedings against the chief secretary for contempt of the House after he skipped the meeting called by the committee.
Members of the Question and Reference Committee said that they would also initiate "forgery proceedings" against Prakash for misinforming the court.
An AAP MLA had yesterday said, "We have learnt that the CS has moved the High Court challenging the breach of privilege notice served to him by accusing us of arm-twisting him in a matter related to alleged attack on him, but he is hiding the fact that the meeting was related to rising NPAs."
"The committee members challenge the CS to stick to the contents of his affidavit and not alter these contents. The chief secretary is clearly trying to shield those involved in the multi-crore scam, which appears to be on the lines of the Punjab National Bank scam," the committee had said in a statement.