The helicopter scoured the area around the centre in Oakham Road, Greetham for 10 minutes but found nothing and left at 12.35am.
Police believe the break-in happened at about midnight.
A garden centre representative said: "We were broken into and they stole two safes. There is damage to a window."
Rutland police commander Kam Mistry said: "We believe there would have been a vehicle involved so we are asking anyone who saw something at that time to come forward."
Anyone with information can contact police on 0116 222 2222.