Armstrong told Britain's Daily Mail newspaper in an interview published Monday that Verbruggen insisted "we've got to come up with something" to explain his positive tests for a banned corticosteroid.
Cycling's governing body, the UCI, appeared to ignore its own anti-doping rules when it accepted Armstrong's backdated prescription for a cream to treat saddle sores.
That allowed Armstrong to continue in the race and he went on to win the first of his seven Tours, helping revive the sport after doping scandals wrecked the 1998 Tour.
"The real problem was, the sport was on life support," Armstrong was quoted telling the newspaper. "And Hein just said, 'This is a real problem for me, this is the knockout punch for our sport ... so we've got to come up with something.' So we backdated the prescription."
Though Armstrong has acknowledged the prescription excuse in a television interview with Oprah Winfrey, he had not previously linked Verbruggen or other UCI officials with a coverup.
Verbruggen, who served as UCI president until 2005, did not respond to phone messages on Monday.
The Dutch official, who is still listed by the UCI as its honorary president, has long denied any collusion with Armstrong despite widespread claims the American rider was protected.
Verbruggen was granted honorary membership by the IOC in 2008 after 12 years' service, and will complete his duties as chairman of the Olympic Broadcasting Service after the Sochi Winter Games in February.
The IOC responded cautiously to Armstrong's allegations.
"It is hard to give any credibility to the claims of a cyclist who appears to have misled the world for decades," the Olympic body said in a statement Monday. "That said, the UCI is currently working on plans to investigate the matter more thoroughly and we await proper considered outcomes from this investigation rather than on rumour and accusation."
Armstrong spoke out while the UCI is in the process of creating an independent commission that will examine alleged official collusion, and he is expected to be the star witness.
Armstrong, who is seeking a reduction in his lifetime ban, told the Daily Mail that he would reveal details of how the UCI operated.
"I have no loyalty toward them," he said. "In the proper forum I'll tell everyone what they want to know. I'm not going to lie to protect these guys. I hate them. They threw me under the bus."
In October 2012, the UCI decided not to challenge a U.S. Anti-Doping Agency verdict to strip Armstrong of his Tour titles and ban him for life. Verbruggen's successor, Pat McQuaid, said the disgraced rider deserved to be forgotten by the sport.
The UCI has been led since September by British official Brian Cookson, who defeated McQuaid in a presidential election where the Armstrong case and cycling's doping past were central issues.
In a statement Monday, the UCI said its commission would "invite individuals to provide evidence."
"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," the governing body said. "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."