Angela Smith, Minister for the Third Sector, gave the figure to Parliament this week in response to a question from Jeremy Hunt, shadow culture secretary.
Jenny Willott, the Liberal Democrat spokeswoman for charities, said: "This is a ridiculous sum of money to spend on three Christmas trees. You can get perfectly good ones for about £40.
"The Cabinet Office is supposed to be cutting back on waste wherever it can and prioritising spending on front-line services and support, especially for charities – not wasting thousands on Christmas decorations.
"They had better be the biggest and most beautiful Christmas trees in the world for that price. Shame no one will be in the Cabinet Office over Christmas to enjoy them."
Ben Wittenberg, director of policy and research at third sector training organisation the Directory of Social Change, said staff at his organisation had contributed to a £10 tree from Asda.
"The amount seems slightly absurd," he said. "Plenty of small organisations in the voluntary sector would kill for £3,000, particularly at this time of year."
A Cabinet Office spokesman told Third Sector: "Like many workplaces, the Cabinet Office pays to have Christmas trees in its buildings.
"The cost covers the delivery of each tree from a certified sustainable supplier, the decorations, installation, maintenance and disposal in an environmentally friendly way."
The Cabinet Office has 1,359 staff. Last Christmas, it spent £5,700 on trees.
A spokesman for Hunt said he had asked several departments about their spending on trees and the Cabinet Office was "at the higher end of the scale".