He said there had been a "deliberate misunderstanding" of his earlier remarks on the subject.
Speaking at the Centre for Excellence in UK farming conference, Kendall said: "The challenge is more complex and difficult than just lifting agricultural productivity. When we say that it must be stepped up, that does not mean at the expense of the environment."
He stressed that the NFU remained "100 per cent committed" to the Campaign for the Farmed Environment. But he added: "If, in 40 years' time, biodiversity in Britain is no worse than it is now, that will be a fair achievement. If productivity is no better 40 years from now, we will be in deep trouble."
Kendall had earlier said at the Agricultural Industries Confederation annual conference: "We face the prospect of seeing an area the size of Northamptonshire mothballed as a result of proposed Common Agricultural Policy reforms. Yet Defra ministers seem to remain interested in transferring money away from food production and towards the environment."
He claimed then: "We haven't got a biodiversity crisis in this country. Most of the key environmental indicators have been moving in the right direction and almost 70 per cent of farmland is covered by an agri-environment scheme. What we do have is a productivity crisis."