Milligan out for six weeks for surgery
The setback comes as fourth-placed Victory prepare to face Western Sydney Wanderers at AAMI Park on Tuesday night.
Another winless round could see Kevin Muscat's struggling team slip to seventh on the table, with Adelaide United, Sydney FC and Newcastle Jets each just one point behind.
They are already without suspended marquee centre-back Pablo Contreras and Mitch Nicholls has been ruled out with a knee injury.
Adding to the player shortage, Scott Galloway, Jason Geria, Connor Pain and Nick Ansell are all away on international duty with the Australian under-22 side.
Milligan missed the Victory's 1-1 draw with Newcastle Jets on Friday night due to the injury with Leigh Broxham taking over the captaincy.
"Following a recent recurrence of the injury, the club's medical team decided it was best the surgery be undertaken as soon as possible to ensure Mark will be back on pitch ahead of a busy end of season schedule," the club said in a statement.