Six men have been arrested after 638 dead protected birds and one otter were found in their possession.
Four eagles were among the cache.
A further 251 birds declared to the authorities were unaccounted for.
Tools used for embalming, two chest freezers, cartridges and weapons were found.
The searches were conducted in Siggiewi, Rabat, Safi, Zurrieq and Kirkop.
The six men arrested were aged between 23 and 42. They are expected to be arraigned in court in the coming days.
The arrests were the result of an investigation by Police Administrative Law Enforcement officers and the Specialist Enforcement Branch of Wild Birds Regulation Unit.
Police investigations are ongoing.