The case has gained notoriety throughout the country since the first threatening letter arrived in November.
Naima Amzil and her boss had been called heroes for refusing to cave in to demands from a group calling itself New Free Flanders, which insisted the woman be fired because she is Muslim.
Amzil, originally from Morocco is one of some 400,000 Muslims in Belgium. Authorities say it is unclear why she was singled out by the extremists.
"I can assure you that we put all means at the disposal of the investigators to catch the perpetrators and the investigation will not stop until the moment we catch them," said Prime Minister Guy Verhofstadt.
Even King Albert II received Amzil and delicatessen factory owner Rick Remmery at the Royal Palace to show his support.
Amzil gave up on Wednesday when she heard of the latest letter, which contained two bullets and warned that "the execution is being prepared again". It added that Remmery's gourmet products would be poisoned.
"I can assure you that we put all means at the disposal of the investigators to catch the perpetrators... "
Belgian Prime Minister
Remmery, who employs 50 people in rural West Flanders, pleaded with Amzil to stay but said "the pressure had become too much for her".
In the letters, Remmery has been threatened with arson and murder. One put a 250,000 euros (US$340,450) price on his head because he employed a Muslim woman who wears a head scarf.
Remmery refused to fire the worker or demand she remove her scarf. One morning, Amzil did so herself, saying she did not want to put her colleagues at risk. Still, the letters kept coming.