Hunters will only have to renew their license every five years as opposed to annually, Animal Rights Parliamentary Secretary Roderick Galdes said.
Addressing a press conference, Mr Galdes said the government had changed the system to "reduce bureaucracy".
Hunters will make significant savings under the new licensing system.
Mr Galdes said certain sections of the licence were now 50 per cent cheaper. Most licences will now cost €50 and applications can be made at MaltaPost as from next week. Licences for rabbit hunting will be about €25.
Mr Galdes said the old licence was simply a receipt against payment which was inserted in the Carnet de Chasse, the hunters' catch reporting booklet.
The new card, however, looked like and ID document and importantly included a photo to help in law enforcement.
Mr Galdes also announced a new hunting reporting system.
He said the Carnet de Chasse system, a booklet which hunters submit annually and is checked manually, was being scrapped for an "avant garde" digital one.
Hunters would now be given cards with all legal hunting species and corresponding codes. Hunters would then report catches to a new digital system using their telephone and the data will then be compiled in real time.
Sergei Golovkin who heads the Wild Birds Regulation Unit said the new system would help law enforcement as police would be able to check hunters' catches against real time data. It will also mean that the information will not take months to be compiled and can be shared with stakeholders faster.
In a statement this afternoon, Birdlife said it was pleased that only the proposed administrative changes had come into force.
It said it was in discussion with the ministry concerned and was hopeful of finding ways to stop the Conservation of Wild Birds Regulations from being weakened.
"While the reduction of fees for hunting licenses is a political decision, BirdLife Malta has already made clear with the Parliamentary Secretary its concerns about the new system for registering hunting catches.
"These include the fact that checks in place to ensure that hunters are adequately reporting their catches, will now more than ever rely on the enforcement afforded by the already stretched ALE unit within the Malta Police Force," it said.
Birdlife said it was also concerned that the electronic game reporting system fell short of providing information on hunting effort.
It said that in the old carnet de chasse system hunters were obliged to also record hunting days when no catches were made, a valuable statistic useful for authorities to report on hunting seasons and derogations.
"It appears the new system will not cater for collecting this valuable statistic which would otherwise help authorities gauge the latest trends in hunting effort," Birdlife said.