"If there's new evidence, whether from inside or outside (Indonesia), he will be charged again," said Harsanto, a secretary to security minister Susilo Bambang Yudhoyono said on Thursday.
The Supreme Court on Tuesday announced that it had halved a three-year jail sentence on Bashir for immigration offences and document forgery. A lower court last September had cleared the cleric of terrorism charges.
Foreign governments have accused Bashir of leading al-Qaida-linked Jemaah Islamiyah (JI) group, which is blamed for the Bali bombings of October 2002 and a string of other deadly attacks.
US Homeland Security Secretary Tom Ridge, speaking after talks with Yudhoyono on Wednesday, said Bashir was deeply involved in terrorism and the court ruling was disappointing.
"Hopefully in due time, at some point of time he will be brought to justice in a different way," Ridge said, without elaborating.
Bashir is expected to be freed in early May.
Britain's Financial Times newspaper, quoting an unnamed senior security official and diplomats, said on Thursday police and prosecutors were examining how to bring new charges against him.
Abu Bakr Bashir says claims
against him are US/Jewish slander
Jakarta has urged the US to provide access to top terror suspect Hambali, who was arrested last August and is in US custody, saying his information is crucial in unravelling terror cases involving alleged JI members in Indonesia.
Harsanto said Bashir's current case could continue if Bashir or prosecutors ask for a judicial review of the Supreme Court decision.
However a spokesman for the Attorney General's office said prosecutors had accepted the Supreme Court decision and the case is closed.
A national police spokesman declined comment on whether police would launch a fresh probe.
At Bashir's original trial prosecutors alleged he headed JI, authorised the network's church bombings in Indonesia which killed 19 people on Christmas Eve 2000 and plotted to blow up US targets in Singapore.
Last September Bashir was convicted of taking part in a JI plot to overthrow the government but judges said there was no proof he had led the network. They jailed him for four years for treason and for immigration-related offences.
An appeal court in November overturned the treason conviction but said Bashir must serve three years for immigration and forgery offences.
The cleric co-founded an Islamic boarding school from which several convicted terrorists graduated. He says claims that he is linked to terrorism are part of a US and Jewish smear campaign against Islam.