It has written to the councils after members of the public complained about heavily branded comms, such as stickers on wheelie bins and banners on refuse-collection lorries.
Durham County Council has also received a warning.
The referendum concerns the abolishment of the region’s two-tier government structure that comprises county and district councils. It will offer voters to choose between a single body and a system of three unitary authorities.
An Audit Commission spokesperson said: ‘We have written to the councils reminding them of their obligations under the Local Government Act 1972 but have taken no formal action.’
The ballot closes on 14 November.