Judge Maria Servini de Cubria ordered on Monday that a lawyer and an accountant be installed at the AFA for three months to look at alleged irregularities in its management of match broadcasting funds.
The order, which included suspending a proposed AFA presidential election on June 30, met with resistance from board members who threatened to withdraw Argentina from the Copa that kicks off on Friday.
However, AFA president Luis Segura denied the team would be flown home.
"I'm not resigning and there is no possibility of the national team returning from the United States," he told a hastily-arranged news conference on Tuesday.
"There is no possibility the football will stop, nor that Boca Juniors won't play the Copa Libertadores," he added referring to the July semi-finals of South America's elite club tournament that the Buenos Aires-based team are favourites to win.
"I hope this (order) isn't the start of Government intervention (in the AFA)," added Segura.
World football's governing body FIFA does not favour state intervention in football affairs.
Argentina, captained by Lionel Messi, are favourites for the Copa tournament that marks the centenary of the world's oldest international football competition.
They begin Group D action against holders Chile in California on Monday. They also face Bolivia and Panama in the opening round.
(Reporting by Luis Ampuero; Writing by Rex Gowar; Editing by Tony Jimenez)
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