Harry Lennon suffered a fractured toe in the 3-2 defeat to Doncaster Rovers on the opening day of the season.
The centre back had an X-Ray on Monday which confirmed the fracture, and he will undergo a scan in the next 24 hours to reveal how long he will be sidelined for.
Blues boss Chris Powell said: “It’s disappointing for Harry to have suffered an injury at the start of his Southend career. His absence will provide an opportunity for somebody else to step up.
“We wish Harry a speedy recovery and hope to see him back on the pitch as soon as possible.”