The current account deficit widened to a record high of 5.4% of GDP in the September quarter as export growth slowed more sharply than imports, with a similar gap expected in the December quarter likely to prolong weakness in the rupee.
The current account deficit is expected to stay at record high for the entire 2012-13.
Rajan was speaking at the convocation ceremony of a banking and finance institute in the western city of Pune.
He also said food inflation persisting at a high level was not easy for the central bank to manage.
India's annual consumer price inflation accelerated to 10.79% in January from the previous month, government data showed.