Many of the EU criminal justice treaties which the UK is a member of will cease to apply if there is a hard exit this autumn.
And a no-deal Brexit could lead physical structures along the border which could under attack from dissident republican terrorists.
Garda Commissioner Drew Harris said members of his force would work with the PSNI to mitigate the impact of a no-deal Brexit.
He warned: “We want to make sure that we’re still able to share information but if one thinks that the treaty that we will fall back to was written in 1959 – so 60 years of improvement is going to fall away in terms of the development of criminal justice cooperation across Europe.
“So it’s not going to be the same. We can’t make it the same until there is some agreement between the United Kingdom and the EU on cooperation (in) criminal justice matters.
“It is of concern.”
Extradition proceedings to send suspected criminals from one jurisdiction to another have been well-established.
The European Arrest Warrant has helped police on both sides of the border to intercept suspected fugitives from justice.
Use of the EAW is one provision which has been debated before in the context of Brexit.
EU chief negotiator Michel Barnier has warned the UK would be forced to leave a scheme which is pivotal to law enforcement across Europe.
Mr Harris is a former deputy chief constable of the PSNI.
He said: “The sharing of information, the joint operations will all carry on – investigations will carry on – and I know the chief constable of the PSNI and myself are not going to sit idly by and allow a threat to just develop.
“We will be acting and will be acting decisively and conducting investigations, and seeking intelligence and following through on that – we are not idle bystanders just watching this.
“People can be assured that we do all we can to protect the people of Ireland.”
He said a lot of the criminal justice treaties that the UK is presently a member of will fall away from the UK.
“That that is not going to simplify policing.
“But we are in constant operational contact with our colleagues in the PSNI, but also across the Irish Sea to the United Kingdom’s National Crime Agency (NCA).
“Our relationships are good. We’re working through what the specific issues might be but at the same time the UK, through Brexit, is losing access to a lot of the EU’s criminal justice treaties and the investigative provisions that they apply.
“We can’t avoid that and we have to mitigate that as much as we can in terms of our operational work with the PSNI.”
Over the last 18 months the Garda has built up resources at the Irish border, the UK’s only land frontier with the EU after the divorce, and will continue to do so.
Mr Harris added: “We are dedicated to making sure that that remains an area where the rule of law applies.
“We will be there to keep people safe, will be there to deal with smuggling as we are at the moment, our organised crime as we are at the moment and the threat from terrorists.”