Nabiullina said the figure took into account so-called quasi-budgetary expenditures in the form of subordinated loans to business, which would be repaid at a later date.
"The real deficit will be less," she said.
Russia's economy grew 8.1% in 2007 and the government expected GDP to grow 7.8% in 2008 but had to lower its forecast to 5.6% due to the global financial crisis.
Finance Minister Alexei Kudrin earlier said Russia's GDP growth would be close to zero and budgetary revenues could decline 40% in 2009 amid the economic crisis.
The federal budget for 2009 originally set expenditures at 9.024 trillion rubles ($250 billion at current exchange rates) and revenues at slightly over 10 trillion rubles ($277 billion), but the drop in oil prices has cut the expected income dramatically.
The budget was based on an average oil price of $95 per barrel for the year, but is being recalculated based on a figure of $41 per barrel.