Glasgow and Edinburgh city councils said they were disappointed the Climate Change Adaptation Programme consultation failed to address key areas including who would pay for preparations to cope with global warming.
The consultation found the "over-arching aim" of the plans to make Scotland ready for the fall-out from climate change had been widely welcomed by a range of correspondents, including councils and environmental bodies.
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But some local authorities said lack of detail on funding was a critical omission, while environment quangos raised concerns over the impact of coastal erosion and fears that city centre pollution and urban temperature hot-spots had been overlooked.
Action plans are being formulated to help deal with health effects of climate change and the impact on businesses, as more severe weather patterns could bring cold winters that would affect older people, and warmer weather lead to new illnesses.
One example might involve training farmers on how to introduce different crops if climate change affected traditional crop growing.
Floods, new pests and diseases and migration - as people move to higher ground - could have significant effects on Scottish society and its economy, according to government findings.
Glasgow City Council, a Labour-led administration, said in its response to the consultation: "There are some good ideas and some valuable policies but, overall it seems a short-term plan, rather than the flexible, long-term approach that Scotland will need if it is to successfully become a 'climate-ready nation'.
"Simply identifying action planned or proposed in the next five years will not be sufficient."
Edinburgh City Council, which is a Labour/SNP coalition, responded: "The role of local government in adaptation needs to be better emphasised.
"The City of Edinburgh Council is a major player and, as such, significant funding will be required to fulfil the conditions of the adaptation programme.
"There is no mention of how actions in the programme will be funded. Climate change impacts will place immense strains on public sector budgets."
The Convention of Scottish Local Authorities (Cosla) said: "Understanding the risk of flooding does not ensure that action is taken to mitigate the risk. For the most part this requires financial input."
A Scottish Government spokesman said it was "showing leadership" on the issue. He added: "All responses to the public consultation on the draft programme will be taken into consideration."