The Spaniard, who captured her maiden major crown by beating Serena Williams in the Roland Garros final last June, suffered a thigh injury in Brisbane.
That is the latest setback for what had looked to be a burgeoning career.
Success in Paris came a year after Muguruza reached the Wimbledon final but she's struggled with the tag of Grand Slam champion around her neck.
Early losses at Wimbledon, the Olympics and the US Open in the second half of 2016 saw her slip down the rankings from a high of two.
With a record showing she's yet to go beyond the last 16 in Melbourne, there is little to suggest the 23-year-old will be holding the trophy aloft later this month.