A two-year-old girl was found by police in the room, but she was not injured. The children have been placed in the custody of the Children Youth and Families Department for a minimum of 48 hours.
Local animal control officials were also called to remove two pit bulls that were discovered in the motel room.
Police said that the parents could face charges of criminal negligence for allowing a loaded gun to get into the possession of a child.
The District Attorney's office will be notified and will decide whether to press charges.
The case is strikingly similar to a shooting in December last year, when a woman, 29, was fatally shot by her two-year-old son in an Idaho Walmart, after he found a gun in his mother's handbag.