Howman, in an address to an anti-doping conference in London last week, had said urine analysis had not advanced much over the decades and that testing was not catching the real cheats.
"We're still in a position where we're getting the same number of positive cases each year, and many of them are in the category of what I call the 'dopey dopers' - the inadvertent dopers, or the ones who are just darned stupid," he said.
Professor Peter van Eenoo, director of the WADA-accredited laboratory at the University of Ghent, said Howman had got it wrong.
"It's incredible that somebody said this," he told Reuters in a telephone interview. "What he says is the percentage of positive samples hasn't changed much over the years. And therefore science has not made any progress.
"What he completely forgets is that for every step of progress we made, of course, the others adapt."
Richard Ings, former head CEO of the Australian Sports Anti-Doping Authority, also tweeted in support of Howman's assertions.
Howman, who left the World Anti-Doping Agency (WADA) in 2016, is now chairman of the Athletics Integrity Unit board and has previously criticised his former employers for failing to support clean athletes and for allowing the reinstatement of Russia's anti-doping agency.
Van Eenoo said the substances being used, the doses and how they were being used by drugs cheats had changed over the decades.
Data from re-testing, using urine samples from the 2008 Beijing and 2012 London Olympics, had also demonstrated the advances of science.
"There were about 10,000 samples, 25 positives. What they've done is stored all those samples and re-tested 1,000 of these negative samples," he said.
"Out of those 1,000 samples, 100 at re-testing later turned out to be positive. That is only through scientific progress, because nothing has changed. It's the same urine.
"And because they know we can now detect substances for a longer period, they (athletes) switch to other substances or take them in smaller doses. So they adapt everything and that is only pushed by scientific progress."
Van Eenoo said urine testing, first introduced at an Olympics in 1968, had its limitations but would remain the 'gold standard' for some time to come.
He accepted that some substances, such as growth hormone, were hard to detect in urine and that blood was a better indicator of the effectiveness of drugs.
"That's why we are now investing in looking into blood concentration -- dried blood spots, those kind of things -- to complement urine," he said.
"If we are looking at a zero tolerance policy which is important for most of the substances and especially those which are most performance-enhancing -- steroids, EPO -- then urine is the gold standard and will remain for quite a long time to come."
Van Eenoo said it was difficult to look for 400 or 500 substances in a drop of blood.
"So that's why I'm saying urine as a first and then for some of these substances where you have issues... you can re-analyse that drop of blood only for one or two substances," he added.
"This makes absolute sense and we need to progress in that direction. That's additional scientific progress, it doesn't mean that the scientific progress we've made so far doesn't exist."