The concerns came amid Sportscotland plans to reduce sport funding in Scotland by 20%.
Scottish Athletics, which runs the initiative to encourage non-club runners to take exercise, said it was shocked by the decision.
The Scottish government said £50,000 had been provided last year to help JogScotland become more sustainable.
The scheme has been in place since 2002 and has evolved into a network of over 300 clubs with about 40,000 members.
Of those who joined a JogScotland programme, 68.6%  were previously inactive, most were over 40 and 77% were female.
Every Tuesday night, JogScotland's Leven group, known as "Leven Las Vegas" has met at the local swimming pool before heading out on a social jog, walk or run.
Malcolm MacTavish, 61, who is one of the group's regulars, said five years ago he weighed 100kg and was on the maximum dosage of blood pressure tablets.
He said: "One day I just stopped and said I had to do something about it and I looked around for ways to improve my health and came across 'Couch to 5K'.
"Within a year I had lost a third of my body weight and was off medication totally."
In the aftermath of the Olympics and the Commonwealth Games, Scottish Athletics said the initiative was a key priority.
The organisation's CEO Mark Munro said the decision to pull the funding was not theirs.
"We're absolutely devastated and shocked as well," he said.
"We received a £100,000 from the government roughly for the last number of years and for a reason unknown to ourselves, the funding has been cut."
He said less than 20% of Scottish Athletics budget was spent on elite athletes with the majority being used to support clubs, coaching and development pathways.
The Scottish government said it was "making significant investment in sport and physical activity" and that the funding for JogScotland was never direct.
A spokesman said: "In 2016/17 Sportscotland provided Scottish Athletics with £65,000 to create a digital pilot system to demonstrate the impact which the JogScotland programme is having, and to use this to generate commercial income.
"An additional £50,000 was provided by Sportscotland to further support the transition of the JogScotland programme to a more sustainable model.
"In terms of the budget allocations for 2017/18, Scottish Athletics will discuss with Sportscotland how they plan to carry forward their strategic plan and their priorities for the forthcoming year."
The initiative is now in discussions with mental health charity SAMh about the possibility of a funding partnership.
JogScotland Fife group leader Ian Shield, said he did not mind where the funding came from as long as the "important resource" was not lost.
"The way I look at it, we get about 40 people here on a Tuesday night," he said.
"People see 40 people dressed up to go running. I see 40 people who in 20 years time won't be lying in an NHS bed trying to recover from diabetes or circulation problems, heart problems, obesity.
"That's what I see."
JogScotland's future could be at risk after it emerged £100,000 of Scottish government funding is to be cut.