It is believed three to five small motorcycles were travelling east through a shopping centre car park on Hall Road when one of them struck the woman about 5.10pm.
Investigators were told the small motorcycles failed to stop and left the scene.
The 34-year-old Carrum Downs woman was airlifted to The Alfred hospital where she remains in a critical condition.
The boys, a 16-year-old from Carrum Downs, a 17-year-old from Seaford and a 15-year-old from Carrum Downs, are assisting Major Collision Investigation Unit detectives with their enquiries.
Police executed a number of warrants at houses in Carrum Downs, Seaford and Frankston today.
A 17-year-old Frankston North boy was also interviewed by police last night and has been released pending further enquiries.
Police are still searching for an outstanding person in relation to the incident.
Anyone with any information is urged to contact Crime Stoppers on 1800 333 000 or submit a confidential crime report at www.crimestoppersvic.com.au