"Natural England is now working to assess these to offer agreements to those applicants who have submitted high quality plans that will do most to improve our water quality and the farmed environment, including for our birds and bees."
Around 11,000 farmers have come out of Entry Level Stewardship agreements in 2015 and these would have been the prime target for CSS Mid Tier agreements.
Natural England had planned capacity to deal with a maximum of 8000 Mid-Tier applications in the first year of the scheme and had allocated a budget for 4,500 new agreements.
The spokesperson said: "We needed to ensure that there would be sufficient delivery resources available to deal with applications and that we had sufficient budget available under the Rural Development Programme.
"We did not assume that we would necessarily receive this number in practice and so we remain pleased with the quality and volume of applications received for the first year of a new scheme."
She said it was too early to estimate how many of the 2,314 applications would result in agreements next year but said the agency would work with applicants where the application has fallen just short or there has been a ’simple error’.
However, a number are likely to fall by the wayside in what is a competitive scheme. "It is a competitive scheme so it will be the best ones that get through."
Responding to criticism the scheme was inaccessible to many upland farmers who had previously relied on Uplands, ELS, she said: "BPS payments in the Severely Disadvantaged Areas (SDA) and the lowlands were equalised in 2015 and the moorland rate was almost doubled.
"This will distribute direct payments more equitably across English farms, and ensure that upland farmers with large areas of moorland are not put at a disadvantage with respect to other upland farmers."
She said the agency had published additional scheme guidance recently and was ’trying as the scheme develops to simplify it’.
The agency had three years to spend the money allocated to the scheme this year before it would have to be sent back Brussels, she added.
The Country Land and Business Association blamed the ‘failure’ of the scheme to attract sufficient numbers on the ‘chaos’ of its introduction and its ‘onerous requirements’ put in place by Defra and Natural England, which it said had discouraged landowners from participating.
It warned the natural environment and the wildlife would ’pay the price for the failure of the scheme’.
The association predicted the number of agreements offered would be far lower than the number of applications received due to the competitive computerised scoring process.
CLA president Henry Robinson said: “The chaos of the new scheme’s introduction and the complexity of its requirements have put land managers off participating next year.”
Last week, Mr Eustice claimed all was well with the scheme.
He said: “We have had good interest in this scheme, exactly where we expect it to be – thousands of applications and expressions of interest.”
He denied it had been made more complicated than ELS, blaming the additional CSS burdens on European Commission auditing requirements and refuted claims under-pressure hill farmers who have struggled to enter CSS had been disadvantaged by the scheme.
Mr Eutice said CSS funding was always going to be targeted at smaller numbers of farmers who could make the biggest difference to local environmental priorities, such as water quality or farmland birds.
But NFU vice president Guy Smith said there was ‘huge disillusionment’ with the scheme among farmers.
He said: “We have done a survey and farmers really don’t like it. They think it is badly designed and badly launched and they don’t trust the small print.
He said ’thousands upon thousands’ of farmers who had previously embraced stewardship were set give it up.
“This is not about farmers walking away from Countryside stewardship. It is about Countryside Stewardship walking away from farmers," he said.