Europol says the horses came from various places in northern Spain or Portugal and their identification was forged by modifying their documentation and microchips.
Authorities in Belgium, France, Italy, Portugal, Romania, Switzerland, Britain and Spain co-operated in the operation.
A Dutch national has been arrested in Belgium and authorities suspect that he is the mastermind behind the operation.
He has been sought since a scandal in the Republic of Ireland in March 2013 when horsemeat was found in beef burgers.
"In Spain, 65 people were arrested and charged with crimes such as animal abuse, document forgery, perverting the course of justice, crimes against public health, money laundering and being part of a criminal organization", Europol said in a statement.
The scam hit fast-food restaurants and frozen food shops who had no idea the products contained horse meat.
As per investigative agencies, the meat was not fit for human consumption.
Horses in bad shape, too old or simply labelled as "not suitable for consumption" were being slaughtered in two different slaughterhouses, Europol says.
The spokesman explained that officers launched a full-scale probe, called Operation Gazel, after detecting "atypical signs in the horse meat trade" previous year.
The European police agency Europol said 65 people were arrested in Spain, and the main suspect, a Dutch citizen, was arrested in Belgium.
Investigators searched for the origin of the contamination and tracked it to the Dutch man. "From there he led the activities of the organisation, putting his most trusted men in charge in every country affected by the scam".
He was subsequently arrested in Belgium.
The Spanish police led the operation, with the assistance of Europol.
A spokesman said: "As a result of the police operations, several bank accounts and properties have been embargoed and five recently-purchased high-end vehicles seized". Further investigations showed that meat sold in ready-made meals in many British supermarkets consisted of anything up to 100 percent horsemeat.