"WADA has no evidence of other international federations (IFs) 'discussing atypical blood test results, or other test results' with athletes," the global agency said.
Verbruggen, the International Cycling Union (UCI) president from 1991-2005, was quoted by Dutch magazine Vrij Nederland as saying it had informed dozens of riders including Lance Armstrong over the years if they had recorded suspicious test results.
"It used to be the UCI's policy - and indeed also of other federations - to discuss atypical blood test results, or other test results, with the riders concerned," Verbruggen said on Wednesday.
"Riders who were doping (but had not failed a test) were effectively warned that they were being watched and that they would be targeted in future with the aim of getting them to stop doping."
But WADA, which has been at loggerheads with UCI over the disgraced Armstrong, strongly questioned such a practice.
"This approach totally contradicts the purpose of an effective anti-doping program, which should be designed to deter, detect and prevent athletes from doping," it said.
"Furthermore, any IF that would do such a thing would leave itself open to criticism with regards to its impartiality and integrity."