The former Scotland international suffered the damage during his team’s 3-2 Ladbrokes Premiership defeat by Ross County on Saturday.
A brief statement on the club’s Twitter account read: “Kevin McNaughton has undergone surgery on his Achilles following the injury sustained on Saturday. Full prognosis is not known at this time.”
A ruptured Achilles can keep a player out for between six and nine months.
It is the latest injury blow for the 33-year-old, who had only played five games in the 21 months prior to making his Caley Thistle debut in July, having overcome knee and hamstring problems.
The former Aberdeen, Cardiff and Wigan player had been featuring at centre-back in the absence of Josh Meekings, who has not played this season because of a knee injury, but has now returned to training.