Elin Jones said preparations for a pilot badger cull were proceeding
A three-year £27m programme to eradicate bovine TB in cattle has been outlined by the assembly government.
All cattle herds and individual cows over 42 days old will be tested but there is no cull of wildlife, such as badgers, that carry the disease yet.
Rural Affairs Minister Elin Jones said she would make a statement on plans for a pilot badger cull early next year.
She warned the disease "continues to escalate and needs to be tackled" to protect wildlife and the national herd.
The cost of compensating Welsh farmers for TB in cattle has soared by 59% in the past year, up from £6.3m in April to September 2007 to more than £10m in the same period in 2008.
Between January and May 4,600 this year cattle were slaughtered, compared to 3,200 in the same months in 2007.
The assembly government said it was seeking a "clear, accurate and detailed analysis of the scale and scope of the disease in Wales".
Ms Jones said: "The TB Health Check Wales will start on 1 October and means 3,500 additional herds being tested in a period of 15 months ending on 31 December, 2009.
"In effect this means that in 15 months we will be testing herds that would have normally taken four years to test.
"To date, Wales is the only area of the UK that has taken this decisive action, part of a meticulous, step-by-step campaign constructed in Wales to remove this damaging and costly disease."
In April the minister announced a "targeted cull" of badgers, with the location and details of the cull to be decided.
She denied there was any "scaling back" of that plan.
"The research has been commissioned, it's happening and I've said that I'll be making a further statement on this in the early New Year," she said.
Animal campaigners have described the intended cull as "misguided" and held protests in Bridgend, Cardiff, Haverfordwest, Lampeter, Llandysul, Porthmadog, Swansea, Wrexham and Oswestry on Saturday.
The UK government has decided not allow badger culling in England, warning it could make the bovine TB problem worse.