Home Secretary David Blunkett has called the resignation of Immigration Minister Beverley Hughes "the worst personal day".
Blunkett had backed Hughes
He said Ms Hughes had resigned because of a discrepancy in her reply to a letter from Labour MP Bob Ainsworth.
Mr Blunkett said that it was a mark of her honesty that she was determined to go.
The home secretary blamed the media climate and said in other circumstances a minister would not have resigned.
Mr Blunkett was Ms Hughes's boss in the Home Office.
He insisted on Thursday he still had "absolute confidence" in her, adding she was a "highly-competent, able, honest" minister and her departure was a "personal blow" to him.
He said she feared there would be questions over her integrity if correspondence between her and Labour's deputy chief whip Mr Ainsworth surfaced.
"She believed so strongly that her integrity mattered to her and to the government that she should offer her resignation," he said.
The resignation follows weeks of accusations that immigration applications were being approved without the normal checks.
The Conservatives have repeatedly been calling for her to go.
Downing Street says she left after it had become clear she had given a "misleading impression" to Parliament about the running of her department, "albeit unwittingly".