Trapping sites visited by BirdLife teams last Saturday were found to be targeting finches and golden plover, the organisation said.
It said in a statement that 40 active sites were visited by four teams who found 24 sites illegally targeting finches and 14 golden plover through the use of exceptionally large nets, artificial ponds, decoys and illegal tape lures.
It was not possible for the teams to determine the target species of one of the other sites. One site targeting song trush, a legal species to trap.
"Saturday's surveillance follows BirdLife receiving numerous reports of illegal activity throughout Malta and Gozo within the last few weeks.
"Following BirdLife reports, five individuals were apprehended by police and video evidence will be submitted by BirdLife to assist police in their investigations."
BirdLife said that two illegal finch trappers at Benghisa Fort on Saturday had been reported to the police by BirdLife a month before, which resulted in their equipment being confiscated.
Despite this, they had continued illegal finch trapping activities. These two individuals were seen on Saturday, disguising themselves with a balaclava and picnic blanket as they collected their equipment and left the sites before the ALE arrived.
BirdLife teams also witnessed several incidents where song thrush cages were used to disguise illegal trapping activities, sometimes just before police arrive on the scene.
"Song thrush nets have also been used at a site in Zurrieq, but the trapper was targeting finches using live decoys.
"At Qala, a trapper was seen replacing golden plover decoys with live song thrush cages when he realised a BirdLife team was present."
BirdLife said trappers were taking advantage of the open song thrush trapping season to illegally target other species.
"With only one ALE vehicle usually available on Malta and none on Gozo, it is impossible for the unit to address such widespread and high numbers of illegal trapping sites," conservation officer Nicholas Barbara said.
Malta, he said, is already facing infringement proceedings by the European Commission for allowing trapping since joining the EU, as the Commission feels that Malta's trapping does not meet the conditions required under EU law.