Mr Chouhan purportedly made the controversial statement while addressing a meeting of the BJP's state executive committee in Bhopal on Saturday.
The chief minister he would "hang officials upside down" if he found that revenue matters not under dispute were pending for more than a month.
He made the remark when a party leader from Bundelkhand region raised the issue of revenue matters pending for long, and sought Mr Chouhan's intervention to cut delays.
While the Congress slammed Mr Chouhan for using harsh words to warn officers, BJP leaders neither confirmed nor denied the statement though they maintained the CM talked about taking tough action against officials who delay clearing files without any valid reason.
"The chief minister is serious about farmers' issues. He talked about taking tough action against those who delay disposal of revenue cases of farmers," state BJP spokesman Rajnish Agarwal told PTI when asked about Mr Chouhan's controversial remark.
The opposition Congress accused Mr Chouhan of shifting the blame for his government's "failures" to bureaucrats.
Congress leader Jyotiraditya Scindia said in a statement that the chief minister's strong words against officials showed his desperation.
"There is rampant corruption in the revenue and agriculture departments. Farmers are in trouble because of the wrong policies of the BJP government, but the CM is trying to escape responsibility and blame officials for the current state of affairs," said the Lok Sabha MP from Guna.
Some officials have been working with Mr Chouhan for the the past 11 years. The CM is now blaming them for his "failures" as his support base is shrinking after the farmers' agitation last month, Leader of Opposition Ajay Singh told reporters.