Justice secretary Michael Matheson said there was a “real danger” the ability to track down and apprehend criminals overseas would be weakened as a result of Brexit.
He was speaking yesterday following an EU justice summit attended by organisations including Police Scotland, the Crown Office, the Law Society of Scotland and Scottish Government Brexit minister Mike Russell.
Mr Matheson said the possible loss of access to the European Arrest Warrant would leave Scottish law enforcement relying on extradition arrangements no longer recognised by many EU countries or forced into creating new bilateral agreements.
The UK’s future use of the arrest warrant and access to Europol – the EU’s police force - are currently uncertain but likely to be an important part of the exit negotiations.
Under the warrant, EU countries are unable to refuse to surrender citizens who have committed a serious crime.
Prior to the framework coming into force in 2003, extradition in Europe was governed by the 1957 Convention on Extradition.
Mr Matheson said: “European Arrest Warrants are extremely valuable. The quickest we have been able to get someone arrested from the point of issuing a European Arrest Warrant in another country is five hours.
“The average timescale of dealing with those European Arrest Warrants to someone being apprehended is 42 days.
“Prior to having European Arrest Warrants, you had to use extradition proceedings – the average timescale for those was nine months. The challenge now though is that as more and more of the members states operate under the European Arrest Warrant, many of them no longer recognise the original extradition treaty.
“When we come out of the EU, if we are no longer able to utilise European Arrest Warrants, there is a real danger that we will be even worse off than we were before the extradition treaty which then creates real issues about how we extradite these individuals back to Scotland.”
Earlier this month, the Home Office said it would opt in to a new framework which allows for continued membership of Europol.
However, it remains unclear what the UK’s links will be with the law enforcement agency following Brexit.
The UK government has said it is “exploring options for co-operation” for when the UK leaves the EU but that it is too early to speculate on what future arrangement may look like.
Mr Matheson said only the Metropolitan Police made more use of Europol’s resources than Police Scotland among UK police forces.
Mr Matheson added: “We make much greater use of European institutions and European networks than England and Wales do.
“Our justice system is very much embedded in those EU institutions and networks. To lose that would have a negative impact.”
The Home Office did not respond to a request for comment.