"In the case of a 'Brexit', it won't be that the EU is simply a group of 28 countries minus one," Steinmeier told a debate on the future of Europe.
But it could unleash new dangerous dynamics, he suggested, pointing to the case of Northern Ireland.
The minister said that an Irish representative had once told him that the conflict in Northern Ireland was currently quiet "because there are no borders in Ireland."
But if the United Kingdom were to quit the EU, "there will be a border again between Ireland and Northern Ireland. And that could at least have the potential of rekindling a conflict that has seemingly calmed down," he said.
In 1998, the Good Friday peace agreement put an end to three decades of fighting between Catholics and Protestants in Northern Ireland during which more than 3,000 people were killed.
EU Commission chief Jean-Claude Juncker told the same debate that a Brexit would be a catastrophe and said Europe needed Britain's pragmatism.
Juncker said he would not visit Britain ahead of the June 23 referendum, where polls suggest it could be a very tight vote.
"The European Commission is less popular in Britain than it is in Germany," he said, suggesting that "if the European Commission were to actively get involved in the referendum campaign, it could have the contrary effect."