Quotes emerged on Sunday of Higuain reportedly branding three-time Ballon d'Or winner Ronaldo "over-rated" and egotistical in an apparent interview with Spanish magazine Don Balon.
However, Napoli have now insisted that the Argentina international never made such comments about the Portugal international.
"Napoli and Higuain categorically deny ever he has been granted an interview with 'Don Balon'," the statement read.
"Therefore the sentences attributed to Higuain are considered false and without any foundation."
Higuain, who played alongside Ronaldo at the Santiago Bernabeu before moving to Napoli in 2013, made headlines when he was quoted as saying: "He [Ronaldo] has a lot of ego.
"If you don't say he's the best, he's not your friend. Cristiano thinks he's the best but he's over-rated.
"I've shared a dressing room with Messi and one is nothing like the other."
Higuain scored in Napoli's 2-1 victory over struggling Serie A champions Juventus on Saturday.