Sir Stewart, who is now vice-chancellor of Edinburgh University, wrote the teacher training section of the Dearing Inquiry into higher education.
In it, he says he has garnered a "significant amount of evidence that the process of assessment has been less than satisfactory".
"I am concerned at indications that the recent 'sweeps' may have been poorly planned and hurriedly performed I some comments suggest that the HMI inspectors were not familiar with the (OFSTED inspection) framework and may have allocated gradings on uncertain evidence."
He writes that Mr Woodhead's controversial decision last year to reinspect primary teacher training "casts doubt on the objectivity and integrity of the process as well as the objectives."
His report also suggests that the inspection framework may have moved too far towards measuring a "narrow range of competences", and that university departments are being deluged with overlapping requests for audit information for OFSTED and the Teacher Training Agency. The work of measuring standards in teacher education would be managed more effectively by the new Quality Assurance Agency, the report says.