The count accused Hubbell of scheming to conceal work done by him and Mrs. Clinton, his former law partner, on a failed Arkansas land deal.
The judge agreed with Hubbell that the allegations in the count were too vague.
Independent Counsel Kenneth Starr had obtained a 15-count indictment of Hubbell last November in connection with a land deal known as Castle Grande. Federal regulators said the deal was riddled with "insider dealing, fictitious sales and land flips."
Robertson dismissed Hubbell's motions to throw out other counts in the case.
Mrs. Clinton was referred to 36 times in the original indictment against Hubbell, signifying that her name could be brought up repeatedly in the trial set to begin June 14. She could be called to testify.
The Clintons' Whitewater partner, the late James McDougal, tried to sell off pieces of Castle Grande to prop up his collapsing savings and loan.
The dismissed count charged that from March 1989 through December 1995, Hubbell tried to cover up the true nature of his and Mrs. Clinton's relationships with Hubbell's father-in-law, Seth Ward, and with McDougal's Madison Guaranty bank.
Hubbell also was accused of making "false and fraudulent" statements and representations to two U.S. banking regulatory agencies.