Last week, journalist Sami Ibrahim had reportedly filed a complaint accusing Chaudhry of slapping him at a wedding, Dawn news reported on Monday.
A copy of the complaint, that was circulating on social media and was retweeted by Ibrahim, alleged that Chaudhry had slapped and cursed the journalist without any provocation. It also accused the Minister of threatening Ibrahim.
Subsequently, the Ministry of Science and Technology had issued a response, saying that the "incident" should not be treated as a "clash between two institutions but as a conflict between two individuals".
The statement said that Chaudhry had "reacted after another person tried to wound his self-esteem".
"To term a patriotic Pakistani and government office holder as an agent of (enemy agencies) is contrary to moral and journalistic ethics," it added.
According to the Prime Minister's Office on Monday, Khan took notice of the matter and spoke to the journalist over a telephone call.
"The leadership of the Pakistan Tehreek-i-Insaf does not support any personal action (by its members) that hurts another person's sentiments and self-respect," the Office quoted the Prime Minister as saying.
"Government and the media are two essential parts of the democratic process," Khan said, adding difference of opinions should not turn into personal conflict.
A rift between Chaudhry and Ibrahim came to light earlier this month, when the Minister unleashed a Twitter tirade against the journalist for accusing him of plotting against the ruling party, reports Dawn news.
Ibrahim responded to Chaudhry's remarks in a television programme and accused him of using state vehicles for personal purposes during his tenure as Information Minister.
( With inputs from IANS )