Officers were called to the Asda Clydebank Superstore at Britannia Way, near the busy Clyde Shopping Centre, at around 1.55pm on Tuesday following a report that the four-year-old had been assaulted.
It still remains unclear exactly what happened to the boy, who told his mother about the attack while shopping in the store.
Officers are now working to establish the full details of the assault. Additional police are now on patrol in the area.
Police are now looking through hours of CCTV footage in a bid to identify the attacker.
All staff at the store have been interviewed as part of the investig-ation and police are appealing to the public for witnesses.
Detectives at Dumbarton Police Office have asked for any witnesses to come forward with information. Chief Inspector Gail McClymont said: "We have a number of officers dedicated to the inquiry and to reassure the public, have put additional officers on patrol in and around that area.
"I would urge anyone who may have been in the supermarket at that time or who saw anyone acting suspiciously in the store or surrounding area to call Dumbarton Police Office on 01389 822000.
"You can also call us on that number if you spot any suspicious persons or activity in the area."
Chief Inspector McClymont also urged parents to be on their guard.
She said: "We would remind parents to be vigilant at all times."
As Asda spokeswoman said: "We have taken this report very seriously. We alerted the police and are supporting them fully."