Houvenaghel accused the organisation of ageism, adding that coaches had "zero regard" for her welfare and that she felt "oppressed" by former performance director Sir Dave Brailsford and former technical director Shane Sutton.
The Olympic silver medallist said she was "pleasantly surprised" that a leaked draft report into the culture and climate within British Cycling had vindicated the criticisms put forward by the likes of Jess Varnish, Nicole Cooke and Emma Pooley.
Asked if rider welfare was as important as the drive for medals within the programme, Houvenaghel told BBC Sport: "No, not from my own experience. It was medals at any cost, of course. That's how it was whenever I was there, certainly in 2012."
Such a criticism could lead to further questions for UK Sport, which has made Olympic medal success the sole criteria for distribution of funding to sports bodies.
However, Houvenaghel also said some riders within the programme received favourable treatment and might not even have been aware of what was going on around them.
"Certain riders that were chosen and favoured will not have experienced that culture of fear in the same way so they don't really understand," she said. "It's probably quite baffling for them to hear the accounts of people in the same team, that they might not have been aware of the sort of oppression going on."
Houvenagel won Olympic silver in the individual pursuit in 2008, and gold in the team pursuit at the 2008, 2009 and 2011 track world championships, but was "frozen out" of the team in the build-up to London 2012 - something she blamed on her age as she was 37 at the time of the Games.
"I felt it was more ageism," she said. "I was a little bit older than my team-mates and it wasn't something the staff necessarily wanted in 2012...
"After six years of constantly medaling at world cups, world championships, and national championships, both on the track and on the road, they discarded me in a very undignified way. I don't think the fastest team on the day was permitted to race."
Dani King, Laura Trott and Joanna Rowsell-Shand won gold for Great Britain in a world record time in the event.
A draft of the independent review's report into British Cycling, leaked to the Daily Mail, delivered a damning indictment of its "dysfunctional" and "inept" leadership.
"I'm pleasantly surprised that the report seems to have come out as being quite an accurate report," Houvenaghel said. "Obviously a lot of work has gone into research and discussion with many people in order to produce the report. The full report is not in the public domain yet and this is a leaked report, but so far it seems to be quite accurate."
Asked why riders might not have spoken out before, Houvenaghel said: "If you rocked the boat, you were out. I don't think it's that they're scared. I think they're perhaps protecting their futures."
In a response to Houvenaghel's interview, a British Cycling spokesperson said: " British Cycling has acknowledged and takes very seriously previous cultural and governance failings in the world class programme.
"That is why we commissioned the Cycling Independent Review alongside UK Sport and accepted its draft findings and recommendations.
"The 39-point action plan, defined by the board of British Cycling based on the draft recommendations of the independent review panel and agreed with UK Sport and Sport England, will systematically address the cultural and behavioural shortcomings in the world class programme, as well as across the broader organisation.
"Our new chair Jonathan Browning has apologised for instances where we have fallen short in our commitment to athlete welfare and has offered to meet with anyone who can help improve British Cycling."
Already months late, the publication of the final report is due imminently. It has been held up as the individuals criticised within it are given a right of reply.
Read the original article on Eurosport: Houvenaghel: British Cycling's pursuit of medals created 'culture of fear'