The car was found abandoned on Blackbird Close at Bentley Park about 12.45pm by police.
One of the puppies was later found with a 16-year-old boy at an address in Woree about 9.55pm.
He was taken into custody and was later charged with a number of offences including unlawful use of a motor vehicle and entering a dwelling.
Police attended another property in Edmonton hours later, finding a 16-year-old Bentley Park boy alleged to be involved in the theft of the puppies.
One of the puppies was allegedly hidden under a bed.
Police seized the allegedly stolen puppy along with jewellery and clothing from the home.
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The 16-year-old Bentley Park boy was charged with entering a dwelling and receiving tainted property.
Both puppies have been returned to the owner.
Both 16-year-old boys were refused police bail and are scheduled to appear in the Cairns Children’s Court.
Police are still searching for two female puppies.
Anyone with information that may assist police is urged to immediately contact Policelink on 131 444 or Crime Stoppers on 1800 333 000.