Bowman suspended CAO Deepak Joshi on Friday, saying he had "lost confident" in him.
The suspension was to end on Wednesday, but Bowman was granted a request to extend the disciplinary action by another 30 days.
Joshi will be paid during the period of the suspension and Michael Jack will assume the duties in the interim.
Joshi took over on an interim basis last year after former CAO Phil Sheegl was forced out during real estate scandals.
Joshi's appointment was opposed by some members of council, who felt he had been too closely linked to problems with fire hall replacement programs and cost over-runs with the police headquarters project.
So far Bowman has declined to give details on the reason for the suspension.