Bahuguna said he came to know about the fact and "action would soon be taken" against the chairman.
The Uttarakhand CM, who was here to attend a religious function, told reporters that he "was not aware about dozens of cases against Namdhari."
Yesterday Bahuguna had said in Dehradun that Namdhari might be removed.
"His (Namdhari's) tenure is yet to be over. But the state administration will act and find a way out to remove him," the CM had told reporters in reply to a question.
Namdhari was appointed as chairman of Uttarakhand minority commission during the BJP rule in 2010 and his tenure will complete early next year.
His association with Chaddha came under scanner after it was found that he was present along with his PSO Sachin Tyagi, an Uttarakhand Police constable, at the time of the shootout at the farmhouse in which liquor baron Ponty Chaddha and his brother Hardeep were killed.
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The name of Namdhari's PSO has also cropped up in connection with the incident prompting Uttarakhand DGP Satyavrat Bansal to send a team to the national capital to ascertain facts about his alleged role in the incident.
Tyagi allegedly fired a few shots during the shootout to protect himself and his protectee.
A police team headed by Inspector Pramod Shah had been sent to Delhi to find out facts about alleged role of Tyagi, Uttarakhand DGP had said.
He said some cases were lodged against Namdhari in the state.
The DGP, however, added he could not say anything about the type of cases and in which part of the state these were registered.