Dublin Port's decision to restrict cruise ship traffic could result in serious knock-on costs, says Simon Coveney.
He cited Cork, Waterford and Belfast, which have massively benefited from the growth of tourism.
The port has blamed Brexit for its decision to reduce the number of cruise ships allowed to dock each year from 160 to 80.
The port is trying to increase provision for freight and container traffic in the light of the UK's departure from the EU.
The Tanaiste confirmed he has raised the issue within Government because of its potential knock-on cost to other Irish ports.
"Cruise liner traffic has been increasing year-on-year in Dublin, but, of course, there is a space problem for Dublin Port," he said.
He added the port had to prioritise how it used that space in the context of Brexit, with more freight passing through it.
"But I do think there needs to be a further discussion in terms of how Dublin Port can find a way of giving leadership on cruise liner traffic because, of course, that impacts on Cork, Waterford, Killybegs, Dingle and Belfast in terms of attracting more cruise liner ships.
"When they visit Dublin, they will also visit ports around the island of Ireland. So, we do need to try to ensure these decisions are made in the context of the national interest as well as the difficult commercial decisions that Dublin Port has to make given the confined nature of the port facilities that they have."
Dublin Port insisted its cruise liner decision was rooted in commercial pragmatism.
Dublin Port chief executive Eamon Reilly said it had no option but to ration available port capacity given the competition for berth spaces and the looming implications of Brexit.
However, the decision to restrict cruise liner numbers is seen as a blow to ports including Cork, Waterford and Belfast given the boom in the cruise liner trade over the past decade.
Dublin, Cork and Belfast have enjoyed their greatest seasons since the heyday of the 1950s.
Both Dublin and Cork are set to welcome record liner numbers this year.
Cork hosted 92 cruise ships last year and hopes to exceed that figure by 10pc in 2019.
However, any Dublin decision to restrict cruise liner visits will inevitably hit the port and others around Ireland.
So great is the expansion of the cruise liner sector that Cobh, Ireland's busiest liner port, is considering a second cruise liner berth at Lynch's Quay.