"I will take a few weeks off to cross train and put 100% of my focus on the 1500m at the Comm Games."
The 34-year-old also said it was the first time he had an injury on that particular bone.
Willis will be seeking his fourth Commonwealth Games medal after winning gold in Melbourne (2006) and a pair of bronzes in Delhi (2010) and Glasgow (2014).
The Gold Coast games will be held on April 4 to April 15.
Sad to withdraw from the @NBIndoorGP this weekend as I have developed a stress reaction in my fibular. I will take a few weeks off to cross train and put 100% of my focus on the 1500m at the Comm Games. @gamupdates@adidasrunning@AthleticsNZ