Hartlepool-born Murphy has broken a bone in his right foot and will be out for at least two months. He picked up the injury in training this week.
With the new season just five weeks away it means that Boro could have a problem filling the left-back role for the opening games. Franck Queudrue is suspended for the first five games of the season, with Murphy being the obvious choice to replace him.
Boro may now look to stalwart Colin Cooper, who is currently in talks regarding a new contract, to fill the role.