The amnesty, granted by the country's Parliament, was expected to end the trial of Desi Bouterse and 24 associates, who were charged with abducting and killing 15 prominent political opponents of his dictatorship in December 1982.
"The law must be allowed to run its course," Rutte said.
The three judges hearing the case against Bouterse decided Friday to postpone the trial until May 11 while they review the amnesty law and consider their options.
Attorneys for the president and his co-defendants argue that the amnesty should put an end to the proceedings but prosecutors said the matter must be reviewed by a constitutional court.
Complicating matters is the fact that Suriname's constitution establishes a constitutional court but the country has never created one.
Bouterse has said the amnesty will let his South American country resolve lingering bitterness over its military dictatorship and civil war.
"This is a new beginning," Bouterse said during a visit last week to neighboring Guyana. "This amnesty is intended to heal the whole nation, not just one part of it."
Rutte said his administration is halting government-to-government aid to the former Dutch colony. He did not say how much money was involved, but earlier this week Foreign Minister Uri Rosenthal suggested it amounted to (EURO)20 million ($26.3 million).
Rosenthal said the aid targets Suriname's government and not its 500,000 population. Last week, Rosenthal recalled the Dutch ambassador from the capital Paramaribo to protest the amnesty.
Bouterse seized power in a 1980 coup. He allowed the return of civilian rule in 1987 but staged a second coup in 1990. He stepped down as military chief in 1992, but has remained a powerful force in Suriname. Lawmakers elected him president in 2010.
He has defended the amnesty by pointing out that it also covers the killing of 19 soldiers by rebels in the southeastern region near the border with French Guiana during the 1986-92 civil war.