All animals are stunned before being slaughtered at the Public Abattoir, when they were aimed for general consumption or through the halal ritual.
In the case of halal, the ritual was performed by a Muslim butcher in line with Muslim procedures, the government said in a statement.
The government was referring to a recent comment made by Imam Muhammed El Sadi, who insisted that the slaughter of animals without stunning, done according to the Jewish and Islamic traditions, was "a matter of religious freedom and human rights which should be respected and considered".
His comments had sparked a furore on social media, most of which were against the idea.
The government said in its statement that once carcasses passed through the slaughter-line procedure, they were checked by the veterinarian and individual samples were taken to the laboratory for testing. They were then stamped with the Public Abattoir’s health mark. All carcasses carried a label with information for traceability purposes. Halal carcasses passed through the same procedure, but the label would be also marked “halal”.