The Blues are currently sixth in the table, while Rowett led them to a 10th-placed finish last season after taking over from Lee Clark in October 2014.
The 41-year-old, who also enjoyed success at Burton, is now a wanted man but Birmingham director Panos Pavlakis has issued a statement on behalf of the club's board confirming they expect Rowett to stay at St Andrew's.
It read: "Birmingham City Football Club would like to put an end to recent speculation by confirming that Gary Rowett remains as manager.
"Gary is fully committed to the Club and likewise the Club is fully committed to him.
"We are all keen to put any uncertainty to bed and look forward to the continuation of the great work Gary has done since his appointment.
"Fans can rest assured that everyone at the Club is together as one striving for further improvement and success, with Gary at the helm as manager.
"The board will continue to fully support Gary in every way it can in trying to restore this great Club of ours to a position where we all want to be."
Birmingham face Huddersfield on Saturday on the back of successive league defeats.
