Subject advisory panels were set up ahead of the STFC's 2009 exercise to set its funding priorities for the coming years. But some subject communities, particularly in nuclear physics, still felt that they lost out.
There has also been widespread dismay among astronomers about the STFC's decision to withdraw from several northern hemisphere telescope facilities.
A recent report by the Commons Science and Technology Committee criticised the "adversarial" relationship between the STFC and researchers.
John Womersley, director of science programmes at the STFC, said the existing subject panels had given "extremely useful" input in 2009 and the need for them had been reaffirmed during internal STFC discussions.
But he said changes in the funding landscape since then, such as the creation of the UK Space Agency, meant that it was right to look again at their composition.
Professor Womersley also admitted that the council was "still learning how to interact best with communities" and wanted to "give an opportunity for communities to tell us what they think is working and what could work better if we made some changes".
He said the STFC also hoped to introduce more uniformity into the way the panels operated "so that we have clearer expectations and they have clearer ideas about how their advice is going to be used".
"This is an evolution, not a revolution," he said. "But given the sensitivity of the STFC's relationships with its communities, we think it is important to do it through consultation."
The STFC has also announced that it is to amalgamate its three existing science committees, which provide scientific advice to its governing council, into a single "science board".
According to Professor Womersley, this streamlined structure would provide clearer advice and connection with researchers, as well as saving more than £100,000 a year.