"We reject the '2-for-1' concept and we reject that it be applied to crimes against humanity," cabinet chief Marcos Pena told radio Nacional.
He was referring to the ruling that an offender's prison sentence must be reduced by the time spent in custody awaiting trial, with each day served in detention being counted as two days in the calculation.
The decision could affect around a thousand people convicted for dictatorship-era crimes, and another thousand being held pending outcomes of trials.
"We consider the '2-for-1' to be a symbol on impunity in Argentina," Pena said, arguing its scope should be limited to a handful of cases at most.
The Supreme Court upheld the "2-for-1" application last Wednesday, applying it to the 13-year sentence of an ex-paramilitary fighter convicted in 2011 for crimes including torture and kidnapping.
On Friday, however, a prosecutor disputed its application in another case.
Human rights groups in Argentina have denounced the measure.
The Grandmothers of the Plaza de Mayo, a group highlighting the confiscation of babies born to suspected dissidents during the dictatorship, called the court's ruling "disgraceful."
President Mauricio Macri has not as yet expressed his position on the Supreme Court decision.
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