The net income of the Duchy is paid to the Queen
The value of the Queen's private estate has fallen by nearly a fifth due to the impact of the recession, accounts show.
The Duchy of Lancaster - a portfolio of land, property and assets held in trust for the Sovereign - saw a drop of £75m to £322m in the 2008-9 financial year.
But the income the Monarchy received from the Duchy, used to fund her public and private activities, increased by 5.4% from £12.6m to £13.3m.
The Duchy of Lancaster covers 18,700 hectares across England and Wales.
Lord Shuttleworth, chairman of the Duchy's council, said in the report: "We have suffered a substantial fall in the capital value of our assets during the year, principally in the commercial property and financial investment portfolios.
"Against that, we have achieved an increase in the net surplus, delivering £13.3m to the Keeper of the Privy Purse.
"In the year ahead, it will be hard to maintain, let alone grow, the income, with slow take up for empty commercial space, and a heightened risk of tenant business failure."
The Privy Purse is the name given to income from the Duchy of Lancaster which invests its funds in agricultural, residential, commercial and financial portfolios.
The commercial property sector makes up more than a third of the Duchy's investments and its value fell from £155m in 2007-8 to £118m in 2008-9.
The investments in the agricultural sector have weathered the financial downturn with the report stating there was a "minimal reduction" in their value.
During the last financial year, the total cost to the taxpayer of keeping the monarchy increased by £1.5m to £41.5m.
Established over 700 years ago, the Duchy of Lancaster is a body created under Charter, it is completely self-financing and does not rely on any taxpayers' money.