Thompson said construction of the Tauranga Eastern Link was part of the problem, and the culvert supposed to take the water away did not drain fast enough.
The stormwater overflow from nearby subdivisions also contributed to the flooding problem on his and his neighbour's paddocks, he said.
Thompson, who farms 900 cows, said he had to move 500 of his 900 dairy herd off the farm on to a leased block on higher ground nearby to ensure they had enough grass.
"This is the same issue as last time. If we get any more flooding we could have to replant our pastures again at a huge cost, plus there is the loss of production as well," he said.
Bay of Plenty Regional Council councillor Stuart Crosby said a major investigation had been undertaken by the regional council since the last major storm last April to determine whether stormwater arrangements for the TEL may be ineffective in high rains.
The results of the investigation had not yet come before the full council, Crosby said.
NZ Transport Agency senior project manager Wayne Troughton said the agency was aware of Thompson's concerns.
"We will continue to work with the regional council and other relevant councils to understand the catchment scheme and whether the TEL works are having an impact on it."
Troughton said the highway was completed in accordance with the approved plans and consent conditions.
"These investigations will help us determine whether any improvements can be made."