The new law, which came into force Monday has been criticised by religious groups.
But minister for agriculture and food Dan Jørgensen said that “animal rights come before religion”.
European regulations require animals to be stunned before they are slaughtered, but exemptions can be made on religious grounds.
Some Halal and Kosher consumers believe it is acceptable for the animal to be stunned before it is slaughtered, but many others insist that the animal is fully conscious when it has its throat cut.
Condemning the Danish change in the law, Israel’s deputy minister of religious services Rabbi Eli Ben Dahan said: “European anti-Semitism is showing its true colours across Europe, and is even intensifying in the government institutions.”
Al Jazeera quoted the monitoring group Danish Halal, which launched a petition against the ban, as saying it was “a clear interference in religious freedom limiting the rights of Muslims and Jews to practice their religion in Denmark”
Critics also pointed out that in the same country, Marius the giraffe was shot dead by a zoo because he was surplus to requirements for their breeding program.
Last year, British politicians said that they would not be outlawing religious slaughter despite “strong pressure” from the RSPCA and other bodies.
The organisation for the English beef and sheep industry (EBLEX) has called for two different Halal logos - one for stunned beef and lamb and one for non-stunned - to be introduced to allow more animals slaughtered by Halal to be rendered unconscious.
John Blackwell, president elect of the British Veterinary Association and practising vet, supported the idea, saying: “I think the proposals are all about choice – if people want to consume halal and they don’t have a strong opinion about stunning then they have a freedom of choice to do that.
“Our position remains that animals should all be stunned prior to slaughter such as that they’re rendered insensible to pain at the point of death.
“All the evidence I’ve seen and interpreted suggests there is a welfare issue associated to the perception of pain during the period between the throat being cut and the animal’s loss of sensibility.”
Dr Julia Wrathall, head of the RSPCA’s farm animal science department, said: “We want to see all animals rendered unconscious before slaughter.
“Until that time we are calling for clear labelling so shoppers are armed with information that can enable them to make an informed choice about whether they buy meat from animals which have not been stunned before slaughter.”