The Badger Trust announced on Tuesday it had been granted permission by a judge for a Judicial Review against Defra Secretary Owen Paterson and Natural England.
The trust, which lost a judicial review against the pilots going ahead last year, is arguing an independent panel is needed to oversee the pilots this year.
The first year of the pilots was monitored by the independent expert panel (IEP), which concluded the culls had failed to meet their criteria for both effectiveness and humaneness.
It recommended changes to improve their performance in the second year and said these should be independently monitored before any decision is made on a wider roll-out in 2015.
Mr Eustice said there will be ‘independent monitoring and evaluation’ by Defra agencies Natural England and AHVLA this year.
He said: “What we are not having is the IEP again. I am not sure people understand the distinction yet.
“What the IEP did was always going to be a one-off for one year. Last year the very professional and independent people in Natural England and AHVLA were the ones on the ground monitoring things and collecting all the data.
“The IEP’s role was to give us advice on how we should treat that data and the statistical models we should apply. We do not need them to do that again.”
Speaking at the Livestock Event in Birmingham, he said the staff of the two agencies who will carry out the monitoring were ‘decent, honourable people who are independent’.
IEP chairman Ranald Munro has given his backing to the Badger Trust legal challenge.
He said: “The IEP’s report states clearly the rationale for ensuring independent monitoring and the use of the statistically robust sample sizes and analytical methods, as used in the 2013 culls, are followed in further culling exercises.
“If this scientific advice is ignored, the data collected during the proposed 2014 culls will be insufficiently reliable for assessment of humaneness and effectiveness.”
Eustice suggested the pilots were likely to start in autumn this year, subject to Natural England licences, and said the Government intended to role the cull out more widely once it had got the pilots right.
“We have said there were lessons to be learned from the culls last year, We are going to try and improve training of the marksmen and make sure we apply the right effort across the cull zones to make sure there are not patches where we don’t secure the cull.
“It is too early to say what we will do next year. But we are clear there is no example anywhere in the world where the disease has been successfully tackled without dealing with the reservoir of the disease in wildlife.
“Once we get this right it would be our intention to roll the cull out more widely to those areas which are most affected.”
The six-week badger cull licences permit culling to start from June 1.
“Last year we started the culls towards the end of August. The decision about when we start the culls will depend on the contractors on the ground and Natural England granting the licence.
“We don’t need to start in June. Much more likely is something similar to last year. There always challenges if you go too early in the summer as you have shorter nights. In the autumn you get issues around cover and in the winter you get into the closed.
“But our judgement based on last year is that autumn is as good a tie as any.”