Last month, Communities Secretary Carl Sargeant told AMs he was "minded to phase out" Communities First.
But think tank director Dr Victoria Winckler said there was "considerable uncertainty" for the areas they serve.
The Welsh Government said no final decision had been made.
"It's very difficult for the people running Communities First knowing what their future holds but I think the most difficult of all is for the people in the communities who are benefiting from good Communities First services," Dr Winckler told BBC's Sunday Politics Wales programme.
"What happens to the childcare? What happens to the employment projects and what does 'phasing out' mean?
"Organisations who deliver Communities First and the communities themselves are in a real period of limbo.
Communities First spends about Â£30m each year, with more than Â£300m spent since its launch in 2001.
A Welsh government spokeswoman said: "Although the communities secretary has said he is minded to phase out Communities First, no final decision has been made.
"We are currently seeking views on this and how to engage, support and strengthen communities and would urge anybody with an interest to have their say.
"It is too early to speculate on how any new approach might impact on particular areas."
Wales' most deprived communities are "in limbo" as the Welsh Government considers the future of its flagship anti-poverty strategy, according to the Bevan Foundation think tank.