Bedi made the remark a day after the ruling Congress and the opposition demanded her recall.
The MLAs had demanded Bedi's recall for "disrespecting the government and the MLAs besides delaying the developmental works".
Puducherry Municipality Commissioner R Chandrasekaran was replaced yesterday in compliance with Speaker V Vaithilingam's ruling.
Bedi, who is out of station, said the order has been issued without due approval by the competent authorityas mandated under the rules.
Earlier in a communication to her secretary, she had said "The Lt Governor is the competent authority on matters relating to the services of government officers."
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She is expected to return to Puducherry either tonight or tomorrow.
Chief Secretary Manoj Parida had replaced Chandrasekaran yesterday while assigning his role to Director of Art and Culture S Ganesan.
He had also said Chandrasekaran should report to him for further posting.
The MLAs had yesterday sought action against Chandrasekar, alleging that he was acting on Bedi's "directives" to "disrespect" them and the government.
They said he had recently held a meeting with members of self-help groups in Mudaliarpet without informing AIADMK's A Baskar, the local MLA.
The MLA has approached the Privileges Committee seeking action against Chandrasekar for holding the meeting without informing him.
The Speaker had then directed the government toreplace the Commissioner and keep him under compulsory wait till the privilege issue was disposed off.
Ganesan told PTI that he assumed office last night.
Bedi, who assumed office in May last year, has since then been at loggerheads with the respective governments, irked by "lack of cooperation" to her Clean Puducherry mission.
She had even threatened she would quit her post and leave the Union Territory if there was no improvement in the situation.