Defences in 48 areas will no longer be maintained putting 1,300 homes at risk of being lost.
Homeowners say the plan will have a "disastrous impact" and will leave them unable to sell their homes.
Natural Resources Minister Carl Sargeant said some residents could be relocated.
BBC Wales' Week In Week Out programme has found that shoreline management plans for affected areas shows homeowners might be unaware of the risks and the impact the plan will have on the value of their property.
Fairbourne in Gwynedd has already seen a significant drop in house values since the programme revealed in February that 420 homes could be lost in the village by 2055.
The council said it can maintain defences for 40 years, but Week in Week Out has been told that people wanting to buy in the village cannot get mortgages as companies want security for 60 years.
Huw Gosling, who lives in one of 30 seafront homes at risk in Newton, Porthcawl, said he knew nothing of the plans to stop defending homes before he was contacted by BBC Wales.
"That's worrying because the effect that would have on our houses would obviously be quite disastrous as far as we're concerned," he said.
"I would imagine the next stage would be the houses would be unsalable and eventually fall over."
Bridgend council said it had followed communication guidelines and would work with those affected.
Senior coastal engineer Greg Guthrie, who wrote the shoreline plan for Cardigan Bay, Anglesey and Gwynedd, said it would be "daft" to continue to defend some areas and to do so could cause future problems.
Chartered surveyor Philip Wilbourn, who has advised the UK government on the issue, said any plan which states seaside properties will not be defended was bound to have an impact on house prices.
Natural Resources Minister Carl Sargeant said it would be difficult to justify the spending needed to defend some areas in future.
Asked if those affected would be compensated, he said each case would have to be examined individually.
"It might be a cheaper option to support a community to move on," he said.
Week in Week Out is on BBC One Wales, Tuesday, 28 October at 22:35 GMT.
Thousands of people living on the coast could see the value of their homes fall as the Welsh government agrees to stop defending some properties from the sea.