The cull areas are thought to be in Gloucestershire and Somerset, but this has not been confirmed.
If successful, the programme could be rolled out to other areas by the end of 2014.
Speaking to farmers at a meeting in Tiverton, Devon, Mr Paterson said: “We cannot keep hauling off 26,000 cattle to slaughter every year. We know what the solution is and I can assure you there will be two pilot culls starting in June.”
“We simply have to prove this method of culling works and roll it out the following year, because we cannot allow this disease to run rampant and destroy our cattle industry.”
Meanwhile, Labour, which has opposed the cull, has been accused by the Conservatives of accepting “cash for policy”.
Labour accepted £50,000 last year from Political Animal Lobby Limited, a company linked to Network for Animals, which campaigned against British farmers who supported the cull.