Changing weather patterns, rising sea levels, and increases in extreme weather events like droughts and floods due to global warming are already destroying habitats, and scientists expect the rate of destruction to increase, it said.
And the species most at risk are those that either can't move and can't adapt fast enough or those that migrate over long distances but find their specialised stop-over points gone or disappearing and their vital food supplies dwindling.
"Although it is thought that no species has yet become extinct solely because of climate change -- the Golden Toad is a possible exception -- many are predicted," the report commissioned by Britain's Department of the Environment said.
The Golden Toad (Bufo periglenes), a spectacularly coloured species which lived on a single mountain in Costa Rica, has not been seen since a lone male was spotted in 1989. Scientists believe rising temperatures may have driven it to extinction.
The report, prepared ahead of the Eighth Conference of the Parties -- the decision making body of the Convention on Migratory Species -- in Nairobi next month, calls for urgent in-depth studies to identify the main species at risk.
"The report is sobering. It shows very clearly the devastating effect that climate change will have on migratory species," said British biodiversity minister Jim Knight.
Birds, seals, penguins, polar bears, fish, whales and reptiles are among the thousands of threatened species.
"Migratory species, by travelling large distances, being subject to a wide range of environmental influences and relying on a wide range of natural resources, are particularly likely to be affected by climate change," the report said.
And while rising sea levels could drown breeding grounds for some mammals, warming seas could shift fish distribution as temperature-sensitive staple foods like plankton disappeared.
It could even wipe out species through gender mutations.
"Sex ratios of hatchling turtles are dependent on temperatures and increased warmth could potentially lead to all-female populations," the report warned, adding that Sperm Whale fertility also reduced with higher water temperatures.
It said global surface temperatures rose by 0.6 degrees centigrade during the 20th century, with rainfall rising in mid and high latitudes and seas levels rising as ice caps melted.
The International Panel on Climate Change said global average temperatures could surge by nearly six degrees by 2100 with unimaginable consequences.
The report noted that rainfall patterns in Africa were changing -- with dire consequences for migratory birds which wintered there as well as for the humans that tried to eke out a living in the same areas.
Sea ice is retreating as well as thinning in the Arctic, diluting the salinity of the ocean, which affects the density-driven circulation of the earth's oceans, a key element in the determination of the earth's climate.