John Jay received more votes than George Clinton, but on technicalities the votes of Otsego, Tioga and Clinton counties were disqualified and not canvassed, giving George Clinton a slight majority in the official result.
The canvass committee disagreed on whether to allow these ballots to be counted or not. The question was referred to the United States Senators from New York, FederalistRufus King and Democratic-RepublicanAaron Burr, for arbitration. King said all votes ought to be canvassed, Burr said that the ballots from Clinton County ought to be allowed, the ones from Otsego and Tioga counties should be rejected. Thereupon, a majority of the canvass committee (Gelston, Tillotson, Smith, Graham, Van Cortlandt, McCarty, Havens) rejected the ballots from all three counties and declared George Clinton duly elected governor by a majority of 108 votes.
The minority (Jones, Roosevelt, Gansevoort, Sands) protested in writing. In Otsego County, John Jay had a majority of about 400, and discounting the small majorities for Clinton in Tioga and Clinton counties, would have won the election. Clinton was accused by the Federalists of usurpation and the canvass committee of having made a partisan decision against the wishes of the electorate.