Speaking in the European Parliament on Wednesday, McGuinness spoke of the "grave and serious consequences" that would follow for the economy on both sides of the Irish border if the UK does not remain in the single market.
The senior Sinn Féin official told a news conference that "armed groups" were positioning themselves to take advantage of the current "uncertainty" about Britain's withdrawal from the EU.
McGuinness, who was visiting Brussels to meet EU leaders on the impact of Brexit on Ireland, also accused former UK Prime Minister David Cameron of a "very cavalier" approach to the wishes of people in Scotland, Wales and Northern Ireland.
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He said, "I warned Cameron at a meeting last year that he was sleepwalking towards an EU exit. He told me he was confident the Remain side would win but I was never confident of this. He totally disregarded such warnings."
His comments come after UK Prime Minister Theresa May said that she would trigger article 50 by the end of March 2017.
McGuiness added, "The economies of both Ireland and Northern Ireland depend very heavily on EU funding for agriculture and other sectors and this is going to be put at risk because of Brexit. The economy has benefited to the tune of millions of euros thanks to EU membership.
"The British government, however, seems intent on a hard Brexit meaning no access to the single market. This policy appears to have set it on a direct collision course with the EU.
"The prospect of a hard Brexit has already sent shockwaves throughout Europe and would result in grave and serious damage to our economies. There will be co lateral damage to Northern Ireland."
"For this reason, we are arguing that Northern Ireland should be treated as a special case and that includes retaining its membership of the EU. Let's remember that, as in Scotland, the vast majority of those who voted in the EU referendum in June voted to remain in the EU."
He also fears Brexit will be used as a catalyst by "those who oppose the peace process and want to plunge us into the past."
He added, "My message is that we are not about to abandon Northern Ireland."
McGuinness, a former IRA chief, said he will take part in a joint ministerial council meeting in London later this month with political leaders from Scotland and Wales, where he will raise his concerns with Theresa May and the government's Brexit team.
He said, "Her government seems intent on driving us out of the EU even though the majority of people in the North voted to remain.
"No consideration has been given to their needs and wishes and, for that reason, we are calling for the island of Ireland to be treated as a special case. We have a special relationship with the EU and this must be respected.
"We face very difficult and challenging negotiations on Brexit. They will be trying and contentious but any attempt to impose hard borders between the north and south of Ireland will be very fiercely resisted."
Among those McGuinness met were ALDE group leader Guy Verhofstadt, head of the European Parliament's Brexit negotiating team; European agriculture Commissioner Phil Hogan - an Irish national - and Polish MEP Danuta Hubner, Chair of Parliament's constitutional affairs committee.
He also met the leaders of the main political groupings in the Parliament and other senior MEPs.
Meanwhile, Matt Carthy, a Sinn Féin MEP, said British immigration problems should be the "least of Ireland's worries, given economic and social turmoil caused directly by the referendum result."
He said: "The Irish government and a succession of its representatives have been deferential to the British government from time to time. What we are saying is that this is not an occasion for this.
"We need to be pointing out the needs of this island and making demands for the Irish people. It is not their job to be pushing for the wishes of the British government.
"Brexit has presented a huge amount of challenges for the Irish government in terms of the trading relationship with Britain, both to the UK and between Northern Ireland and Ireland. To add on the task of immigration controls, I think is ridiculous."