Disgraced cyclist Lance Armstrong claimed in The Daily Mail on Monday that Verbruggen was involved in a cover up over a positive test for a steroid in 1999, the year he won his first of seven Tours de France.
UCI president Brian Cookson, who succeeded Verbruggen's successor Pat McQuaid in September, has made an independent inquiry, in conjunction with the World Anti-Doping Agency, a priority and is especially keen to investigate allegations of corruption.
Armstrong, who was banned for life and stripped of his seven Tour titles last year, would be welcome to give evidence, so too would Verbruggen.
A statement from the UCI read: "The UCI's Independent Commission of Inquiry is in the process of being set up and we are in advanced discussions with stakeholders on its terms of reference to allow full investigation of any allegations relating to doping and wrongdoing at the UCI. Further announcements will be made in due course.
"The commission will invite individuals to provide evidence and we would urge all those involved to come forward and help the commission in its work in the best interests of the sport of cycling.
"This investigation is essential to the well-being of cycling in fully understanding the doping culture of the past, the role of the UCI at that time and helping us all to move forward to a clean and healthy future."
Verbruggen has always vehemently denied wrongdoing.
In a letter to the national federations, which Italian website Tuttobiciweb published earlier this month, the former UCI president he wrote: "I have never acted inappropriately and my conscience is absolutely clean.
"With the benefit of hindsight, however, I admit that I could have done some things differently, but I do not accept that my integrity is in doubt."