The warning came as Nicola Sturgeon unveiled funding of £42 million a year for flood protection projects across Scotland over the next decade.
The First Minister said the support package would give councils certainty to proceed with local plans to tackle flooding and protect homes as she returned to Newton Stewart, Dumfries and Galloway, which was badly hit by flooding in December.
But Citizens Advice Scotland said research it is carrying out into the issue has uncovered growing problems for Scots trying to secure cover.
Policy manager Keith Dryburgh said: “One of the issues we are already finding is that the cost of insurance for flooded homes and businesses is often un-affordable.
“Indeed, many people have told us that they are actually priced out of insurance because the premiums are so high, so they choose not to get insured at all, while others struggle with their finances due to high insurance payments.
“So while the announcement of more funding for flood mitigation is very welcome, it is equally important that consumers are able to access affordable insurance for when something goes wrong.”
But Alastair Ross, head of Public Policy for Scotland at the Association of British Insurers, (ABI) said climate change is increasing the risk of “more frequent and severe flooding.”
He added; “Further investment and a strategic approach to managing the risk are essential. The devastating flooding that caused disruption to hundreds of Scottish homes and businesses last winter is a reminder of how important the right protection is.”
The Scottish Government said the agreement reached with council body Cosla would secure 40 new flood protection projects benefiting more than 10,000 families.
More than 130 flood protection studies will also be carried out to help find potential solutions for another 26,000 homes at risk.
Ms Sturgeon said: “Earlier this year I saw first-hand the devastating effects of mother nature as storms battered our communities.
“Seven months on and the community have rallied round and businesses are getting back on their feet and returning to normal.
“However, the implications of the storm will be felt for a while yet and we need to work together to minimise any potential future disruption.”
A spokesperson for Flood Re said: “Flood Re is the national reinsurance scheme established by the UK government and the insurance industry to help people who have been flooded or are in a high flood risk area.
“Where these householders are seeing the cost of their insurance go up they should shop around for the best deal.
“People who have done this have seen significant reductions in their premium and excess levels.
“We would urge those affected to visit www.floodre.co.uk for a list of all those insurers who are offering Flood Re backed policies.”