A crisis involving the AUF and players' union has led to AUF president Sebastian Bauza and his fellow executive board members resigning.
Uruguay president Jose Mujica had withdrawn police from the stadiums of the country's two biggest clubs – Penarol and Nacional – after crowd violence in the Copa Libertadores.
Nacional's meeting with Argentine side Newell's Old Boys in the intercontinental competition was marred by several incidents on Wednesday.
That included several fans and police being injured and over 700 seats being ripped out at the Estadio Centenario.
Sunday's scheduled match between Miramar Misiones and Penarol was postponed due to security fears.
"Recent events demonstrate the need to move aside and allow other political views to make football governable," a statement from the AUF board read on Monday.
Scheduling of matches and negotiations of television rights for Uruguay's 2018 World Cup qualifiers are among the other issues facing the game.
FIFA rules protect the game from political intervention and if the government had something to do with the board's resignation, Uruguay could miss the World Cup.
Oscar Tabarez's side are due to face England, Italy and Costa Rica at Brazil 2014.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.