Plymouth have been forced to close the Mayflower terrace area in front of the main grandstand at Home Park.
Home Park will be all-seated from the start of the new season
Premiership and Championship stadia are required to be all-seater, although Argyle were given three years' grace after they were promoted in 2004.
The Pilgrims did apply to the Department of Culture, Media and Sport for special dispensation to retain the terrace, but this was unsuccessful.
"The club is bitterly disappointed with the decision," a board statement read.
"Secretary of State Tessa Jowell pointed out that even without the terracing, we would still have had sufficient seating to accommodate more than our average home game.
"This, ultimately, appears to have been a persuasive influence on their decision."