Judge Levis Italmir Orellana ordered that the case proceed in private behind closed doors, and "parties to the case no longer will be able to comment publicly," a court source told AFP on condition of anonymity.
The proceedings later can be made public again, but only if prosecutors make an appeal, and succeed, the source added.
In power between 1999 and 2004, Flores was investigated both by Congress and the attorney general's office in the wake of allegations by President Mauricio Funes that he had received the millions in donations from Taiwan without accounting for them.
Flores has said he accepted the money but did nothing inappropriate, passing it on through the proper channels.
Also Read
El Salvador suspects he has fled the country for Panama, which the neighboring country has denied.
Lawyer Oscar Campos, with the Social Initiative for Democracy, was stunned at the judge's move.
"Nobody was expecting this; it runs counter to transparency," he said.