The car is believed to have passed through Wairoa on the day of the robbery.
The vehicle was later recovered, but the three men - described as Māori, aged 18 to 22 and of average height – remain at large.
The police spokeswoman said it is not uncommon for offenders to use stolen vehicles to commit crimes.
"These vehicles may be stolen from nearby the offence location or on occasion from other towns and cities.
"Police encourage people to secure their vehicles at all times and contact police if they see anything suspicious."
The spokeswoman said nobody was injured during the robbery in Gisborne.
Police conducted a scene examination at the store and forensically examined the stolen vehicle, but no arrests have been made.
A CIB investigation is ongoing.
Police would like to hear anyone who saw the silver-coloured Mazda Familia with three men in it overnight on Monday, January 11 to Tuesday, January 12.
The public are urged to contact police on 105 and quote file number 210112/2170.