CHIEF constable Simon Byrne said police are concerned if they believe a Brexit deal threatens the union "the loyalist community has at times shown it can mobilise quickly, bring large numbers of people on to the streets and engage in public disorder in support of their cause".
The PSNI chief said "identity is important" to the loyalist community.
"You can anticipate a lot of emotion in loyalist communities and the potential for civil disorder," he told BBC Newsnight.
The 2013 loyalist flag protest saw disorder on the streets and dozens of police officers injured in Belfast.
"There are a small number of people in both the loyalist and nationalist communities that are motivated by their own ideology and that have the potential to bring violence back on to the streets," Mr Byrne said.
"We need to make sure that we're in a position to thwart that sort of behaviour with the support of the communities and all parts of Northern Ireland."
The agreement secured by British prime minister Boris Johnson with the EU would see new checks on goods coming into Northern Ireland from the rest of the UK.
This has led unionists to warn this creates a new customs border in the Irish Sea and the north being treated differently to other UK regions.
"It's well rehearsed that any hard border between Northern Ireland the Republic will be seen as a return to state institutions by the nationalist community and it will raise the threat of attack towards infrastructure," Mr Byrne said.
"But similarly from the loyalist community... identity is also important... and therefore whatever ends up as a Brexit deal, if there is one that could be perceived in a way that sort of threatens the security of the loyalist community... our concern is also the loyalist community has at times shown it can mobilise quickly, bring large numbers of people on to the streets and engage in public disorder in support of their cause.
"... Similarly if things go a different way, you can see a rising of emotion in the nationalist community a similar threat," he added.
Read more: Loyalists plan 'war of attrition'
