The situation has been compounded by Malta's redeployment of experienced enforcement officers in to other parts of the police force and the systematic harassment of BirdLife Malta's staff and volunteers by the police.
Thirty-five years after the introduction of the EU's Birds Directive, Malta has found itself in a storm of controversy over its shooting of birds using the island as a resting place on their ancient migratory route between Europe and Africa.
Following a series of shootings of rare and protected birds, including white storks, by some of the islands 10,000 hunters, the Prime Minister decided to close the autumn hunting season from 20th September until 10th October.
These dates were chosen because they usually coincide with the peak of migration of protected species over the islands, especially raptors.
There is another, more political reason for closing the season for this amount of time. Veteran Labour Party politician Karmenu Vella has been nominated by Malta and selected by the new European President to be Commissioner with responsibility a mixed portfolio of Environment, Maritime Affairs and Fisheries.
Calm under MEP's fire
He underwent a serious grilling by MEPs on 29th September, generally dodging questions on the conflict between his responsibilities for fishing and environment; the use of bee-toxic neonicotinoid insecticides; and the use of cyanide on gold mining.
With Malta's terrible reputation with respect to bird hunting and trapping also high on MEP's list of concerns, he quickly pre-empted further questioning by stating: "I condemn any illegal hunting."
On moves to 'reform' and possibly merge the Birds and Habitats Directives, he said: "Both these directives were our cornerstone to safeguard our ecosystems and our biodiversity.
"The Birds Directive was adopted in 79 some 35 years ago and it has never been reviewed since then ... there is no idea to deregulate or demote them. We are not revising but only renewing."
But will he be tough on Malta's 'derogations'?
But his performance must be measured by results, not vague reassurances. On 9th October the European Commission will be visiting Malta for discussions with BirdLife Malta, the Maltese hunters federation (FKNK) and the Maltese Government.
High on the agenda will be Malta's two derogations from the Birds Directive, and how they are being implemented. The first derogation allows quail and turtle dove hunting to take place during the spring migration. It is now the only country that allows the spring hunting of these species.
And a new, even more controversial derogation will allow Malta to trap finches - reversing a commitment to ban the trapping of finches forever, made as a pre-condition of Malta being allowed to join the EU in the first place.
A show of strength against the abuses of hunters was therefore politically useful for Malta and Vella - as well as likely to save the lives of countless protected birds that would otherwise be illegally shot.
And in that respect he appears to have been successful, as MEPs failed to press him on the abuses of the Birds Directive which routinely take place in Malta
Tensions increase - and raptor kills
Since it was elected in 2013, Malta's new Labour government has put the demands of hunters above bird conservation and it has systematically weakened the controls on hunting and trapping that existed.
One of the reasons protected birds have been targeted recently is that the government removed a 3pm curfew on hunting during the peak migration of raptors to prevent them being targeted. It was inevitable that this rollback would result in a slaughter of birds.
Only last Tuesday, 29th September 2014, a Short-toed Eagle which Birdlife Malta had been tracking for several days was shot at - and has not been seen since.
The situation has been compounded by Malta's redeployment of experienced enforcement officers in to other parts of the police force and the systematic harassment of BirdLife Malta's staff and volunteers by the police, including the high profile detention of naturalist and TV presenter, Chris Packham in April.
The temporary closure of the hunting season, which usually runs from five months between September 1st and January 31st, resulted in an explosive reaction from the hunting community.
On the day Malta celebrated the 50th anniversary of its independence from the UK, with Prince William as guest of honour, several hundred hunters took part in an illegal protest in the capital, Valletta.
Children, elderly, journalists attacked in violent protests
One brandished an apparently fake shotgun, while others hurled abuse and bottles at government supporters and attacked journalists.
After the protest, a group of 30 hunters then went to Buskett woodlands where 13 BirdLife Malta volunteers and their friends, including a 7-year old child, had gathered to watch the daily arrival of birds of prey to the woodlands to begin roosting.
Instead of quietly enjoying the natural spectacle of raptors coming in to roost for the night, the volunteers were set upon by the hunters.
An elderly gentleman was punched in the face and had to go to hospital for treatment of his cuts and bruises and another volunteer suffered a leg injury. Riot police quickly attended the scene and the volunteers were safely escorted from the woodland.
This is what happens in Malta when the hunting community does not get what it wants.
Hunters will keep up the pressure on Vella - and so must we
This thuggish and disgusting behaviour coincided with a meeting in Brussels organised by FACE, the European Hunters Federation, to discuss the Birds Directive. Two representatives of the Maltese hunters' federation were in attendance.
It is no secret that Maltese hunters want FACE to call for a weakening of the Birds Directive to legitimise the decimation of migrating birds that takes place on Malta every year. This is reflected in this statement on the FACE website:
"Whilst FACE joins in celebrating the success of the Birds Directive it argues that greater recognition should be made of the socio-cultural diversity within the EU. People should not be left out of the equation as it is ultimately the citizens that turn policy into action on the ground."
One possible interpretation of these words is that where a powerful hunting lobby, like Malta's, is determined to hunt wild birds in open defiance of the Birds Directive, the rules should be relaxed to allow them to get on with it.
We must hope that the more reasonable hunters in the federation will continue to argue for keeping the Birds Directive intact.
Any weakening would result in even more unsustainable hunting in Europe, something which is as bad for hunters as it is for birdwatcher and the birds themselves.
Support Birdlife Malta's extraordinary efforts here.
Steve Micklewright is Executive Director of Birdlife Malta.
This article was originally published by RSPB: Conflict in Malta over autumn hunting. It has been edited and updated by The Ecologist.