Sutton Bridge Experimental Unit, which specialises in potato research, said dry conditions in one part of the country and wet soils elsewhere are causing the chasm.
In the East, dry conditions are causing concerns for bruising, while in the West and North prolonged wet soils are increasing the risk of black dot and rots developing.
Harvesting is going well in the east, said head of the unit Adrian Cunnington, but growers need to take precautions against bruising with the dry soils.
"Watch drop heights on harvesting equipment and regulate the amount of soil passing over the web to minimise the chances of damage to the crop," he said.
Wetter weather in the North and West, however, led to plenty of soil on the web, while rain has forced some growers to delay harvesting.
Dr Glyn Harper, a potato pathologist at Sutton Bridge, said that in these parts of the country conditions are similar to last year.
"The main concern is black dot," he said. "The longer the crop stays in the ground, the greater the risk of black dot developing. The key to keeping it in check is early harvesting and, once in the store, a rapid temperature pull-down."
Harper said crops left sitting in warm, wet soils carried extra risk of rots. "We're concerned for any tuber rots associated with Dickeya, a potentially more aggressive form of blackleg species, after the worrying rise of cases on the Continent."
Once in store, adequate ventilation is a must, as is the need to avoid hot spots and condensation developing.
Warm, wet conditions are ideal for the soft-rot bacteria Pectobacterium to cause tuber breakdown.
Fungal diseases such as tuber blight, as well as damage during harvest, often allowed the bacteria to gain a foothold.
"Monitoring is crucial during the critical first few weeks of storage. It is vital ventilation continues until the crop is completely dry," advised Harper.