Minister for sustainable food Lord Rooker insisted his department was one of the biggest spenders on research across all areas of government.
"Defra is second only to the Ministry of Defence in its reliance on science and we employ more scientists than other departments," he said. "But R&D is different from what it was 10 years ago and projects can't last forever. Some institutions want to keep their core seed funding and projects."
But he told the Royal Show conference: "When research comes to an end you are not duty-bound to draw up something just because of the institution. It's down to policy."
Rooker said money was often shifted to other institutions, adding: "The cake is only so big. I'm not aware of a project of fundamental importance that we have not bent over backwards to accommodate."
He admitted that cash was tight, saying budgets had been "a bit flat" in recent years but that Defra would protect "as much as we can despite the severe pressure in the past couple of years".