Senior officers from the Police Service of Northern Ireland (PSNI) and An Garda Siochana met in Dundalk on Wednesday for the Annual Cross Border Seminar on Organised Crime.
Speaking ahead of the seminar, PSNI Chief Constable George Hamilton warned that "the more infrastructure there is at the border, the greater opportunities that creates" for violent dissident republicans and organised gangs involved in cross border crimes such as smuggling.
Mr Hamilton said both police forces have been doing "scenario planning" for post Brexit, but said he did not want to get into "public hypothesis that will fuel the debate".
However, he said that through the infrastructure created with the PSNI and Garda Joint Agency Task Force, there is already a "thought through response (to Brexit) between the criminal justice system in the North and South."
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Ireland's Justice Minister Charlie Flanagan warned that "the imposition of a new range of physical border structures would give rise to a very serious challenge".
"The situation on the island of Ireland must ensure there is no physical structure that would act as a barrier to what is a very strong relationship north and south," he said.
Mr Flanagan insisted that the challenges posed by Brexit can be met.
He added: "It is crucially important that whatever the bottom line is in terms of the UK's withdrawal from the EU, that we continue to have and develop the huge levels of cooperation (north and south)."
Wednesday's 15th annual conference brought together senior police from the PSNI, Garda, National Crime Agency, the Revenue Commissioners, HM Revenue and Customs and government departments.
The agenda focused on emerging crime trends, money laundering, mobile organised crime groups, excise crime and drugs.