The federal court in the western city of San Juan said it viewed the Supreme Court judgement to be "unconstitutional and inapplicable" in a case it was deciding.
Its stance is permitted under Argentine law, where federal judges have leeway in interpreting Supreme Court rulings when it comes to people convicted of violating human rights. Other courts could now follow suit.
But any appeals will go back in the country's highest court.
Carmen Roqueta, an Argentine judge who was on a tribunal handling cases related to the confiscation of babies during the dictatorship, noted yesterday that judges are "sovereign" in making decisions.
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"But when the Court builds jurisprudence it's difficult to go back. Judges have to apply the doctrine of the court unless it has new arguments to go against this ruling."
Argentina's government has already come out against the Supreme Court ruling, which covers sentences for crimes committed during the 1976-1983 military dictatorship. It wants its scope to be extremely limited.
That was applied early this month to the 13-year sentence of an ex-paramilitary fighter convicted in 2011 for crimes including torture and kidnapping.
Potentially, it could affect around a thousand people convicted for dictatorship-era crimes, and another thousand being held pending outcomes of trials.
Already, several inmates incarcerated for such crimes are requesting shortened sentences, including a 78-year-old priest, Christian Von Wernich, who received a life sentence for murder and kidnapping.
Tomorrow, the Mothers and Grandmothers of the Plaza de Mayo, a group highlighting the confiscation of babies born to suspected dissidents during the dictatorship, are to hold a march against the Supreme Court's ruling.
It is also seeking a political trial of the three justices who voted in favor of it.
The UN High Commissioner for Human Rights has urged Argentina to align itself with "international norms.