Most of the confiscations were made in the Pacific, around remote Malpelo and Gorgona islands, two protected natural parks with a great deal of threatened biodiversity, a Defense Ministry statement said.
The Pacific region in particular is home to environmental "multi-crimes," which involve both illegal fishermen and timber traffickers, said Captain Javier Augusto Bermudez, of the Colombian Navy.
Photos released by the ministry show dozens of headless fish regularly collected by authorities.
Fauna and flora off the Caribbean coast are also seriously threatened, Bermudez said.
In rivers such as the Orinoco, whose basin Colombia shares with Venezuela, pink dolphins are also victims of illegal fishing.
Colombian law punishes illegal fishing with up to nine years in prison.
In Colombia, one of the most biodiverse countries in the world, more than 1,400 species live in fresh water and at least 2,000 in the seas, according to the von Humboldt Institute, a civil non-profit organization associated with Colombia's environment ministry.
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