Shelter Scotland highlighted that local authority budgets for homelessness services are not ring-fenced and are vulnerable to cuts.
The housing and homelessness charity said money councils receive from central government to pay for temporary accommodation is going to be reduced from 2017 by being linked to the local housing allowance, given to private renters to help with the cost of their home.
Officials claim the funding uncertainty is a potential threat to Scotland’s 2012 commitment on homelessness - promising a permanent home to everyone who is unintentionally homeless - and is calling for cash for homelessness services to be protected.
The warning comes ahead of the charity’s annual homelessness conference - Funding in the Homeless Sector: Beyond the Cuts - at The Trades Hall in Glasgow on Tuesday.
In Scotland, 35,764 people made a homeless application last year and 10,567 households were provided with temporary accommodation - including 4,923 children.
Adam Lang, Shelter Scotland’s head of communications and policy, said: “We are gravely concerned that austerity cuts imposed on local authorities could put pressure on funding for vital homelessness services.
“Combine that with changes to the way in which councils are funded to provide temporary accommodation to homeless people - significantly reducing the budget from next year - and the picture looks very bleak.
“Scotland has made great strides on homelessness over the past decade and it would be a crying shame to undermine that progress.
“Our annual homelessness conference is bringing together housing and homelessness practitioners from across Scotland.
“It is imperative that, together, we face up to the reality that the cuts will happen and try to find some practical and creative ways of tackling this potentially catastrophic situation.”
Housing minister Margaret Burgess said: “We share Shelter Scotland’s concern about the UK Government’s changes to housing benefit for temporary accommodation.
“Temporary accommodation is part of the strong safety net for households that become homeless and the funding that supports this is vital.
“The Scottish Government will continue to work with local authorities to see how they can meet the challenges of the UK Government’s changes to housing benefits for temporary accommodation.”