Chickens are often stunned with an electrified "waterbath"
The European Commission says new legislation is needed to improve animal welfare at European slaughterhouses.
Current EU rules on animal slaughter are "outdated in many respects," the commission said on Thursday.
Under a new proposal, abattoirs would have to ensure proper training for staff and monitor the efficiency of their stunning equipment.
But current stunning methods would not be banned. The proposal still requires approval by all 27 EU governments.
The new legislation will not take effect until it is approved by the European Parliament and the ministries concerned - a process that could take up to three years.
The commission says each slaughterhouse should have an animal welfare officer.
The "waterbath stunner" used for poultry would not be banned, "despite its welfare disadvantages", the commission said.
Use of carbon dioxide to kill animals would still be allowed, despite the concerns expressed by scientists.
The commission says there is a lack of commercially viable alternatives to those methods of slaughter.
The new proposal defines the scope of stunning and slaughter methods more strictly and states that gas stunning of birds must be irreversible.
"Stunned animals will have to be regularly monitored to ensure they do not regain consciousness before slaughter," the commission says.
Third countries exporting meat to the EU would have to meet similar standards.
But small slaughterhouses will be exempt from some of the provisions.
The proposal also covers the killing of animals for fur, the slaughter of male day-old chicks and culling for disease control purposes.
Every year nearly 360 million pigs, sheep, goats and cattle as well as several billion poultry are killed in EU slaughterhouses, the commission says.
The European fur industry accounts for another 25 million animals.
The lobby group Compassion in World Farming expressed regret that the commission failed to demand alternatives to the electrified water bath and carbon dioxide gassing methods, the AFP news agency reported.
Neil Parish MEP, Conservative chairman of the European Parliament's agriculture committee, welcomed the commission proposal.
"In the UK we already have generally high standards for slaughtering animals, but this is not the same across the EU, where standards are patchy to say the least. We need to level the playing field and these new regulations should help to do that," he said.