Cycling is one of Britain's most successful and heavily funded sports, enjoying huge success at the Olympic and Paralympic Games.
British Cycling was also heavily criticised for "a culture of fear" in an independent review published last month that found failings in governance and leadership following allegations of bullying and sexism.
Howden expressed concern in a statement on the British Cycling website (www.britishcycling.org.uk) that three of the 10 English regions had rejected reform proposals at 'mandate meetings' held to decide how representatives should vote.
"Our 136,000 membership should be in no doubt that what is at risk is not only the funding for the Great Britain Cycling Team but our ability to support the grassroots of every part of our sport in every part of the country," he said.
"Without this funding the sport of cycling could be lost to an entire generation. This is no bluff.
"Table Tennis England chose to reject the reforms and had their Sport England funding suspended. We can’t allow this to happen."
National governing bodies have to be compliant with the Code of Sports Governance to secure government and National Lottery funding.
British Cycling is due to receive 43 million pounds over the period leading up to the Tokyo 2020 Olympics from government funding bodies UK Sport and Sport England.
Former British Cycling chief executive Peter King told the BBC this week that he expected the proposals, which require a 75 percent majority vote, to be rejected.
"My original view was that the members would vote in favour of the proposals because of the threat of losing funding," he said.
"But I think the feeling is now moving the other way, and from the meetings I've attended, I think it's doubtful.
"It's right that we modernise, but there's a sense the changes are too severe, have been rushed through, and that members are losing control, with too much authority residing with the board, not the national council."
Howden warned that failure to vote through the proposals, which include a reduction in the number of elected regional board directors and term limits, risked turning the clock back 30 years or more.
(Reporting by Alan Baldwin, editing by Christian Radnedge)
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