Vera Baird, a junior minister in the Department for Constitutional Affairs, said the judge had "got his formula wrong" when jailing Craig Sweeney.
The paedophile's sentence for the kidnap and sexual assault of a three-year-old girl, which means he could be free in five years, prompted a furious row last week after it was branded "unduly lenient" by the Home Secretary, John Reid.
However, the Lord Chancellor, Lord Falconer, defended the judge, insisting he had applied the law correctly. He said that judges should not be made the "whipping boys" of flaws in the sentencing system.
But Ms Baird - a junior minister in his department - has now reignited the row, apparently justifying opposition claims of a serious rift on the issue.
"I'm critical of the judge for three reasons - one, starting too low; two, deducting too much for the guilty plea; and three, getting the formula wrong," she told Radio 4's Any Questions.
But Ms Baird's intervention was branded "ill-informed, misleading, inaccurate [and] extraordinarily clumsy" by a leading lawyer. Writing in The Independent on Sunday today, Lord (Alex) Carlile QC says: "Ministers should be pillars of what is right rather than mere weathercocks of tabloid opinion."
Officials close to Dr Reid suggested he was determined to scrap the automatic reduction of sentences for a guilty plea.
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