EU Structural Funds were worth over £850 million to Scotland between 2014 and 2020, but no new money will be awarded after Brexit takes effect on January 1.
Westminster has yet to set out the detail of the UK Shared Prosperity Fund that will replace it, although there has been a pledge to match the funding that was provided by Brussels.
There are also concerns that any new scheme will be distributed by UK ministers, instead of Holyrood, which had responsibility for the scheme previously.
Organisations dealing with young people seeking to improve their life chances and offenders trying to get into work are among those reliant on the vital EU funding sources.
Professor David Bell, who heads up the Scottish Government's Steering Group on the replacement for EU Structural Funds, has said any replacement must meet the needs of local businesses and communities in a column for today's Scotsman.
"Timing is now critical - there are less than three months to go until the end of the transition period and therefore of the existing EU funding schemes,” he writes.
"At present, there is no signal of interest from the UK Government, nor of any design proposals that would constitute an appropriate use of taxpayers’ money.
"EU Structural Funds were based on a policy framework set by the EU, but with implementation undertaken by the Scottish Government in ways that met Scotland’s needs.
"A future UKSPF similarly needs to be devolved. Whitehall doesn’t know best when it comes to understanding the needs of communities and businesses in Scotland."
The Brexit transition period ends on January 1, although the existing structural funding streams will be in place for organisations for the bulk of next year. But the uncertainty is a growing concern.
Among the organisations in Scotland affected are Right Track based in the east of Glasgow, which helps up to 500 youngsters annually age between 15 and 18 who have learning emotional and educational challenges, with a view to getting them into work or a place in college. Many come from impoverished backgrounds.
The body relies heavily on EU funding for almost half of its £700,000 annual budget.
Gill Law of Right Track said: "We've benefited from European Structural Funds in its many guises since the mid-90s.
"It was originally around to fill gaps in existing funding pots like the national training programme and local authority funding has all been cut to the bone.
"As a result the gaps are much, much bigger."
Apex Scotland deals with about 5,000 people a year who have a criminal conviction or are at risk of getting one, with a focus on getting them ready for employment.
EU funding accounts for about a third of its £2.8m budget, although this is then matched funded by local authorities. Its work includes the Steps programme, an intensive pre-employability course.
Alan Staff of Apex said: "Most of our staff are reliant on it and the longer we go without us knowing what's going to happen, then staff are going to leave, they are going to feel panicky."