Greenpeace, WWF, the Hellenic Society for the Protection of Nature and the Hellenic Ornithological Society said the strategy was mainly focused on "old-school" dam construction instead of eco-friendly river management favoured by the EU.
WWF head of policy Theodota Nantsou said there were "huge concerns" about several of the proposals made by HVA, a Dutch company advising the Greek government.
"Not only are they massively expensive... but they promise even greater destruction," she told a news conference.
In September, Storm Daniel, a Mediterranean cyclone of unprecedented intensity, unleashed months' worth of rain in just hours on Thessaly, Greece's most fertile plain.
The deluge, which left 17 people dead, destroyed roads and bridges and drowned tens of thousands of farm animals.
The groups on Thursday criticised proposals to dredge rivers, arguing that removing obstacles helps floodwaters flow even faster.
Instead they proposed widening waterways and planting more trees to strengthen the riverbanks.
There are also fears that the reconstruction will revive decades-old plans to divert the Achelous River in western Greece, a project repeatedly struck down by the country's top administrative court.
If the Achelous diversion project had existed last September to send water to Thessaly, the flood would have submerged the city of Larissa, Nantsou said.
In a statement sent to AFP, HVA insisted that its approach was science-based.
The company noted that nature-based solutions have been examined under several EU initiatives, but there is "insufficient knowledge" as to whether they apply to projects of the size required in Thessaly.
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