DUP leader Arlene Foster has said she is disappointed to hear the Taoiseach's office is preparing for Britain to "lose interest" in Northern Ireland.
The Shared Island Unit was set up in Micheál Martin's office earlier this year to "work towards a consensus on a shared island".
Mr Martin said it is preparing for the possibility that Britain may get "turned off" the North.
He acknowledged there are "two distinct political jurisdictions" on the island, adding: "We have to acknowledge the reality of that."
However, he went on to speculate on the potential impact of English nationalism, Brexit and the possibility of Scotland leaving the United Kingdom on the North's membership of the union.
"What happens if England gets turned off Northern Ireland? We've got to be thinking all this through," Mr Martin told the Irish Independent.
"They may just say, 'We're not as committed to it as we were in the past'.
"That may not happen for quite some time yet, but we have to be prepared for all sorts of eventualities."
However, Mr Martin ruled out the possibility of a border poll, describing it as "too divisive".
Mrs Foster expressed her disappointment over the comments, coming only a week after what she described as a positive meeting of the North South Ministerial Council (NSMC).
"A good neighbourly N/S relationship requires consistency," she tweeted. "The Taoiseach's comments are disappointing.
"The principle of consent determines NI's place in the UK. NI will keep moving forward by respecting our diverse identities, not dubious theories."