A vote in next week's referendum to break from the United Kingdom "will raise a number of important and complicated issues that will have to be negotiated," said IMF spokesman Bill Murray.
"The main immediate effect is likely to be uncertainty over the transition to a potentially new and different monetary, financial and fiscal framework in Scotland," he said.
"While this uncertainty could lead to negative market reactions in the short term, the longer term will depend on the decisions being made during the transition, and I do not want to speculate on this."
The pound has already fallen sharply in recent weeks, with the question of what currency an independent Scotland would use in the long term unresolved.