The book, called " Trick or Treatment: Alternative Medicine on Trial" and co-authored with Simon Singh, calls into question much of the evidence backing complementary and alternative medicines (CAMs), and their uses and effects.
"Yes, there is now plenty of evidence, and much of the recent research is reasonably sound, but by no means does all the evidence demonstrate that the treatment under investigation generates more good than harm," Ernst writes.
Flawed methods?
The Alliance for Natural Health questioned Ernst's analytical methods because he was drawing conclusions about CAMs from studies that were in themselves flawed, some of which Ernst had conducted.
"Professor Ernst must know how bad, how unscientific, is much of the literature on which he relies.
After all he wrote some of it.
He should speak out against the deliberate bias in many studies - but that might not boost sales of his new book," said the ANH's medical director, Dr Damien Downing.
The book has received widespread mainstream news coverage with the UK Daily Mail writing: "They have produced a definitive - if controversial - guide to what works, and what doesn't.
It makes indispensable, if sometimes alarming, reading."
Ernst was invited to author a guest editorial in British Medical Journal: Clinical Evidence in which, in a more even-handed tone, he stated : "Patients are being continuously and seriously misled by both sides of the debate on complementary medicine".
He went on to note that mainstream journals rarely published positive findings, giving the impression that little serious research was being done in this field, or that the findings showed complementary medicine to be ineffective or even dangerous.
Real losers "Patients are the real losers in the complementary medicine debate," Ernst concluded.
Dr Robert Verkerk, ANH's executive and scientific director, said: "Evidence-based medicine was always meant to include clinical experience and the patient's view; Ernst has no current experience of either.
He bases his arguments entirely on the so-called scientific literature, which he says himself is biased."
Dr Downing said of 32 homeopathic systematic reviews and meta-analyses on record at the UK National Library for Health, only three showed no effect.
Seven reported a statistically significant clinical effect and six showed a non-significant effect.
The other 16 were found to have "insufficient data".
"One obvious conclusion would be that there still is not enough good evidence; another would be that what evidence there is, points clearly in favour of homeopathy," said Downing.