"That government is best which governs least" is a motto with which Henry David Thoreau opens his pamphlet, Civil Disobedience. It has been attributed to Thomas Jefferson, but no one has ever found it in any of Jefferson's writings. I think an argument can be made that it is not very likely he would ever have made such a statement, because it does not square with his views.
Jefferson was not very fond of abstract, ideological theories of government. His ideas were expressed in the form of practical principles, not in abstract generalities. "All men are created equal" refers to the political standing of people in a society. A government that "governs least" leaves too many questions unanswered. What is least? Less government requires some kind of rational guideline more than just that indefinite statement. Jefferson did not express a belief in limited government as an arbitrary generality; rather, he frequently referred to principles whose effect would be the limitation of government within proper bounds. For example, he believed that government should be shaped by the will of the people. As he wrote:
"It accords with our principles to acknowledge any government to be rightful which is formed by the will of the nation substantially declared." --Thomas Jefferson to G. Morris, 1792.
In other words, there is no indication that his theories of the scope of government were formed apart from its necessary function founded on the will of the people. He believed the people should be free to experiment with government, to add and subtract as they went along. As he wrote to John Adams,
"This I hope will be the age of experiments in government, and that their basis will be founded in principles of honesty, not of mere force." --Thomas Jefferson to J. Adams, 1796.