The Minister had told the Home Affairs Select Committee of MPs Sir David Ramsbotham was cavalier in his reports on prisons and had failed to check his facts.
But Sir Stephen, who held the chief inspector's post for eight years before Sir David was appointed in 1996, said: "I find it hard to believe this business about him making up figures or guessing them. It would be totally out of character.
"I think Sir David is doing a splendid job. It's a very difficult role because you must retain your independence but I think he has done that extremely well and the country should be grateful to him."
Sir David has produced a series of damning reports on jails, exposing scandalous conditions at Wormwood Scrubs, west London, and highlighting the poor treatment of teenage inmates at Feltham Young Offenders' Institution in Middlesex.
But Mr Howarth told the committee Sir David sometimes relied on "intuition" rather than hard facts. In particular, he cited comments made by the chief inspector on the number of drug "barons" in jails and on the costs of carrying out drug tests on inmates.
Mr Howarth's attack was seen by many in prison circles as an attempt to undermine the credibility of the inspector because of government concerns that not all his criticisms are fair.
Sir Stephen said he believed that the strain in relations between Sir David and the government was partly due to intense coverage to his most damning reports while ignoring many of his more positive inspections.
But he believed Sir David was "absolutely right" about Wormwood Scrubs in west London. He added: "I don't think Mr Howarth's criticisms were appropriate unless they had talked to him about this before. This ought to be treated as a private matter in the first place."
The two chief inspectors have much in common. Both their appointments were greeted with cynicism by prison reformers who expected them to be establishment figures who would prefer not to rock the boat rather than expose failings in the jail system.
But Sir Stephen, a former judge, and Sir David, a former army general, both embraced the role with an almost missionary zeal to improve conditions for prisoners, even where such a stance has been politically uncomfortable for ministers.
Sir David's present troubles, which are understood to have left him dismayed and seeking urgent clarification from Mr Howarth, follow a prickly relationship between Sir Stephen and the former Home Secretary Michael Howard.
But Sir Stephen, who is now the president of the national ex-offenders' association Unlock, said: "I never had these public rows with ministers. They just muttered quietly to themselves."Reuse content