The Championship club announced the news in a statement, saying that Mowbray is expected to be out of action for six to eight weeks.
They wrote: "Birmingham City can confirm that Manager, Tony Mowbray, requires medical treatment which means he will be temporarily stepping away from the on-site management of the Club for a period of approximately six to eight weeks.
"Assistant Manager, Mark Venus, will assume temporary responsibility for the team with immediate effect."
Mowbray commented: "Following my recent LMA Health Assessment I have received a medical diagnosis that will require me to receive treatment.
"Undergoing treatment will necessitate that I temporarily step away from the Technical Area as Manager of Birmingham City Football Club.
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"Until I return, my Assistant Manager, Mark Venus, will take temporary charge of the team, supported by coaches Ashley Cole, Pete Shuttleworth and Maik Taylor.
"I will continue to provide advice and counsel while undergoing treatment.
"The Club has been incredibly supportive of me and my family and we are very grateful. I know that everyone will be respectful of our privacy at this time."
Birmingham City Chief Executive Officer, Garry Cook, added: "Our thoughts are with Tony, his wife Amber, and family.
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"We wish him a speedy recovery and look forward to welcoming Tony back to the Club to continue the excellent work that he has started.
"In the meantime, Mark Venus, Ashley Cole, Pete Shuttleworth and Maik Taylor, will be given all the support they need to lead the Club forward."
Mowbray, 60, started the season as Sunderland manager, but was sacked on December 4.
Only out of work for just over a month, he replaced Wayne Rooney at Birmingham on January 8, and his most recent match saw him beat former side Sunderland 2-1.