It showed a decline in fish numbers as deep as 2,500 metres, almost a kilometre below the reach of the deepest commercial nets.
Researchers from Glasgow University said it could be that young fish living in shallower water were being caught.
This could be having a knock-on affect on adult populations, they said.
Dr David Bailey, who led the study, said: "Commercial fishing may have wider effects than anyone previously thought, affecting fish which we assumed were safely beyond the range of fishing boats.
"We were extremely surprised by this result and believe that it has important implications for how we manage the oceans.""
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