The Natural Environment Research Council admitted last week that it could have handled last year's financial crisis better.
The council was called before the Commons science and technology committee to justify its decision to cancel an entire grants round in May last year.
Nerc's director of finance and information systems, David Bloomer, told the committee: "We can look back now and would we have done the same? The answer is no. But we had to make a risk-based judgement and (our audit committee) backed that."
The council cancelled the grants round to redress a deficit of between £9 million and £14 million after problems with the introduction of new accounting rules by the Treasury.
Committee members referred to the situation as a "mess". And MP Tom Harris asked why Nerc had been hit so hard when the other research councils had not had trouble adjusting their accounting.
Nerc's chief executive, John Lawton, said: "We knew the change was coming.
It was when it was retrospectively applied that we got into difficulty."
The committee received evidence from a number of sources expressing misgivings about the focus of Nerc's research priorities. Rob Raiswell, head of the School of Earth Sciences at the University of Leeds, said Nerc was giving only "peripheral attention" to fundamental solid-earth science.
But Professor Lawton insisted that overall funding for the earth sciences had remained the same over the past seven or eight years.
Nerc also dismissed claims by the Geological Society of London that Nerc was "in the process of dramatically reducing the number of earth scientists being trained in the UK".
Nerc did identify a serious national skills shortage in hydrogeology.
Professor Lawton said this would be worsened by the closure of the University of Reading's hydrogeology MSc course.
Birmingham University will soon be the only UK institution with a course in this area.