The government has been criticised for trying to "bludgeon" legislation through Westminster to radically cut RHI subsidies with "minimal political scrutiny".
The cuts will see the annual payment for most boilers fall from £13,000 to just over £2,000.
An equivalent scheme in Great Britain is paying up to £20,000 per boiler.
On Wednesday, shadow secretary of state Tony Lloyd expressed concern that the cuts would result in "casualties".
The Renewable Heat Incentive (RHI) scheme was set up in 2012 to boost uptake of eco-friendly heat systems but huge subsidies led to a potential bill of £490m for Northern Ireland taxpayers.
Mr Lloyd said the proposals were not a "trivial matter" and should have been taken through committee to allow for more detailed scrutiny.
He also described the rate at which the proposals were being pushed through as "breakneck speed".
Independent MP Lady Sylvia Hermon said she had been contacted by a large number of people who were "extremely aggrieved" by what was being proposed.
Northern Ireland Secretary Karen Bradley accepted that the cuts were difficult, but said they were needed to comply with EU rules on state aid and to ensure the scheme was legal.
She said that if the changes were not made, the scheme would have to be closed down and no payments could be made.
It was put to her that the cuts would leave businesspeople in Northern Ireland hugely disadvantaged compared to their counterparts in GB who availed of a similar scheme.
However, Ms Bradley said that both schemes provided the required 12% return on investment and the difference in payments levels was due to different circumstances and costs associated with the running of the schemes in GB and Northern Ireland.
Democratic Unionist MP Ian Paisley said the effect of the changes was to ensure that no-one would sign up to a government renewables scheme for a "generation", because promises on guaranteed tariffs had been broken.
The Commons also heard that the bill was wide open to legal challenge.
Earlier on Wednesday, a County Antrim poultry farmer went to the High Court seeking leave to judicially review the proposed legislation.
Counsel for Tom Forgrave claimed the reductions would be "ruinous", however, they accepted the challenge was premature and the case was relisted for hearing in early April after the new laws had taken effect.
A judge at Belfast High Court acknowledged the speed surrounding the proposed legislative amendments, saying it was "proceeding through the Houses of Parliament a what might be described as a rate of knots".
The debate on the RHI legislation has now ended.
It passed through its Commons stages and now moves to the Lords.
But MPS will not continue to scrutinise the bill and suggest changes before it becomes law.