A series of audits were carried out by the Food and Veterinary Office, which identified significant traceability issues with horses slaughtered for EU export that had originated from Mexico and the US.
The move has been welcomed by Humane Society International (HSI), which stated that the latest audit was a "damning indictment of the horse slaughter industry" and of the Mexican authorities’ failure to act on previous warnings.
It added that the decision could potentially have a positive impact on animal welfare, in that it could "reduce the number of horses suffering in the Mexican slaughter pipeline".
Dr Joanna Swabe, HSI’s European Union executive director, commented: "Banning horsemeat imports from Mexico is long overdue. For years Humane Society International has repeatedly sounded the alarm about horsemeat entering the food chain that does not fully meet EU safety standards.
"As well as safeguarding EU consumer safety, closing our borders to horsemeat from these countries is important for animal welfare, too. Horse slaughter, regardless of which country it is in, is fraught with inherent cruelty."
According to HSI, 87% of eligible horses slaughtered in Mexico for export to the EU, originate from the US.
It added that the use of veterinary drugs such as phenylbutazone, which is banned for use in food animals, is widespread; and that mandatory lifetime medical record-keeping is non-existent in both countries.
The HSI said it would also like to see a moratorium covering Canada, Argentina, Brazil and Uruguay where similar traceability problems with horsemeat exports persist.