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David Kenworthy, chairman of UK Anti-Doping (Ukad), told the BBC: "We've been told to expect cuts of up to 25%.
"Ukad would be in jeopardy if we had large cuts like that because the purpose for which we're here, I'm not sure we could fulfil it properly."
The warning comes in a year when sport has suffered widespread doping claims.
"We've got to have the time and means to try to make up that income if we're to survive - if we don't, the integrity of UK sport is at risk," said Kenworthy.
"That would be desperate. With the amount of money invested in the integrity of sport over the years, to get it to where it is, that would be a huge blow to UK plc."
Last year Ukad, which is responsible for protecting clean athletes, conducted 8,728 tests across 40 sports.
The organisation has a budget of £7m - largely made up of state funding - which is less than when it was established in 2009, but has now been told to plan for a possible further cut of up to 25%.
A government spokesperson said: "The government is clear that Ukad works tirelessly to ensure athletes and sport are clean, and continues to be recognised internationally for its work.
"Decisions on future funding are rightly for the spending review on 25 November, but we have also been clear that all parts of the public sector will be required to find savings through efficiencies and reforming the way things are done, so that we deliver more with less.
"It's part our plan to build a strong and stable economy for working people and ensure the sustainability of our priority public services."
But Kenworthy described the proposed cut as "drastic", and added: "Something's got to give, so the testing would certainly go."
"Tests are very expensive. The standard urine sample to be tested costs £371, the athlete biological passport costs £439 for each test.
"I think we'd be almost dead in the water frankly - you can't function on that basis. It would be an appalling cut, and appalling waste of our experience that we have built up. "
As well as testing athletes, Ukad has been investing increasing amounts of time and money into intelligence-based work, joining forces with the National Crime Agency as it looks to cut off the supply of imported, illicit supplements at source.
As part of Operation Bloodthirsty, Ukad has been raiding underground drugs labs in Britain as it tries to crack down on the illegal trafficking of steroids.
"I'd be horrified if we had to reduce our intelligence and investigations because we are dealing there with not just athletes but suppliers, coaches and people encouraging athletes to dope," said Kenworthy.
"Testing is a very blunt tool. So we target test based on intelligence. We're looking at a health problem. People in gyms have no idea what they're buying."
Kenworthy says if its budget is cut, Ukad may be forced to ask the sport industry - which generates billions of pounds annually through sponsorship, broadcasting and tickets sales - to contribute significantly more to the protection of integrity.
"The country can't live beyond its means. We've got to bridge the gap. Sport might have to step up and pay for some of the work that we do," he said.
"Think about the amount of money that goes into sport in this country. Sixty-six medals are forecast for Rio - at a cost of £4.6m for each medal. That's almost our budget - for one medal. If one of those medals if proved to be false the damage done to our reputation is enormous. I'd hate to see the integrity of this country sacrificed.
"The money that goes through our turnstiles is huge, as is the broadcasting rights money. All that money is invested in sport, and the only one keeping us clean is Ukad."
Last year, Ukad analysed 5,160 samples with 0.7% recording adverse findings.
The head of the UK's national anti-doping agency says the body is "in jeopardy" because of potential government funding cuts.