They conveyed to the Home Minister that Dwivedi, who was serving as Joint Secretary (Foreigners) in the Home Ministry, has been "wrongly punished" for the alleged lapses of his juniors, who reportedly facilitated the renewal of FCRA licence of Naik's Islamic Research Foundation (IRF).
Sources said the senior officers, mostly belonging to IAS, told the Home Minister that Dwivedi is an honest officer and such action sends "wrong signal" and is "demoralising" for others.
Dwivedi also separately met the Home Minister to plead his case.
The move by the joint secretaries is seen as unprecedented as there has been no such happening when the bureaucrats joined hands to stand by one of their colleagues, who faced disciplinary action by the government.
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Dwivedi, along with three of his junior officers, was suspended last week after the government found that the FCRA licence of an NGO run by Naik was renewed by the Home Ministry's Foreigners Division headed by him (Dwivedi) despite several probes against Naik for allegedly radicalising youths and attracting them towards extremism.
"It is demoralising for honest officers. I feel injustice has been done to Mr Dwivedi. We have conveyed our feelings," Joint Secretary (Police-I) in the Home Ministry Kumar Alok, who was one of the four officers, had told PTI when asked whether he had met the Union Home Secretary, pleading Dwivedi's case.