Peter Sheridan, now chief executive at Cooperation Ireland said the peace process is in a "fragile state".
He said the numerous agreements that make up Northern Ireland's peace process show the brittle nature of its politics.
"Less than a year ago, both governments had to step in to rescue the executive," said Mr Sheridan.
Although stressing that he did not predict the violence "in the way it was [during the Troubles]", he added: "We've already seen peaceful protests along the border, even though nothing has happened on the border yet.
"The history of this place is that mass protest can lead to confrontation and unrest.
"We've had three shootings in the last few days, so we shouldn't be surprised that there would be people who would seek to exploit a change in the border."
The former assistant chief constable denied that he was scaremongering: "I would challenge anyone who says there won't be people who will seek to exploit the border," he told the BBC's Good Morning Ulster programme.
"We just need to be alert to the possibility that any change to the border, which is largely invisible at the minute, can be seen to threaten people's identity in ways we cannot see."
Mr Sheridan said he believed Northern Ireland Secretary James Brokenshire and Prime Minister Teresa May were genuine when they expressed their commitment to an open border, but pointed out that 26 other countries will have a say on the matter.
A former senior police officer has warned that Brexit could lead to "civil unrest" in Northern Ireland.