New Defra figures showed a rise in incidents for the third year in a row to 936,000, following a decline over the previous 6 years.
Just 2,135 fly tipping incidents, or fewer than one in 400, resulted in a prosecution.
Currently farmers and landowners are obliged to foot the often hefty bills to remove rubbish dumped illegally on their land.
The NFU says it has been sent evidence of "regular, large-scale, co-ordinated dumping", not just of large domestic items such as mattresses and fridges, but also clinical waste and waste from construction and demolition.
It is calling for local authorities and the police to assist landowners in the clean-up and reporting of fly- tipped waste, and for all parties to work together on prevention, clean up and prosecution.
Deputy president Minette Batters said the NFU has now written to the Minister of Justice, Liz Truss, as well as the National Police Chiefs Council (NPCC) and the Association of Police and Crime Commissioners (APCC), to ensure that magistrates are aware of increased fine limits.
"We need a broader government strategy that allows incidents to be reported more effectively and cleared up, intelligence to be shared more easily and we need a campaign to raise awareness among householders on their responsibilities in disposing of unwanted waste," she said.
The call has been echoed by the Country Land and Business Association (CLA). Its president Ross Murray said: "These figures do not tell the full story of this disgraceful behaviour. Local authorities tend not to get involved with clearing incidences of fly-tipped waste from private land, leaving the landowner to clean up and foot the bill.
"Our members have reported a big increase in fly-tipping on their land. It's not just the odd bin bag but large household items, building materials and even asbestos being dumped across our countryside."
The CLA suggests farmers and landowners ensure gates to fields are locked, open up concealed entrances to be more visible to passers-by, use CCTV in black spots and report all instances to the police.