Senior Sergeant Anthony Bond, of Dunedin, said the two batteries, worth $2000 each, were taken from the noise collection station on Monday.
The batteries were being used to power machinery to monitor noise levels.
They each weigh 73kgs and likely would have required two or more people to shift them, he said
The batteries were Ultra branded and a gel deep cycle type, Snr Sgt Bond said.
They are used in heavy machines, solar and motor homes.
Police are asking if anyone has any information regarding this theft, or has seen them advertised for sale, please call 105 and quote file number 231221/7137.