The ministry said the Reserve Fund stood at $44.96 billion on May 1 compared to $50.60 billion a month earlier.
It said it spent $2.6 billion, 2.3 billion euros ($2.63 billion) and 0.4 billion pounds ($578.08 million) from the fund in April.
In roubles the Reserve Fund was worth 2.892 trillion at the beginning of this month.
The Finance Ministry had not depleted the Reserve Fund over January-March.
Russia's government is hoping to keep the budget deficit within 3 percent of gross domestic product in 2016.