"We urge respect for the freedom of religion for foreign workers... and we encourage the workers to complain if their rights are violated," the Labour Affairs Council said in a statement.
The remarks came after prosecutors indicted a garment factory owner and sought an eight-month jail term on charges that she forced three Muslim women workers from Indonesia to eat pork.
Chang Wen-lin, the owner of Hsin Hua Hang company, had threatened to cut their salaries if they refused to eat meals that were also offered to local employees, prosecutors said.
The factory owner, whose permit to hire foreigners was revoked in the wake of the scandal, said she thought that eating pork would provide them with energy, according to legal documents.
The incident surfaced after the three filed a complaint to the Taipei county government saying that they were overworked and had not been paid for around eight months.
Taiwan's mass-circulation United Daily News said the case was widely reported in the Muslim world via international media and dealt a huge blow to the island's image.
There are around 350,000 foreign labourers in Taiwan, largely from Southeast Asia including the Philippines, Indonesia, and Vietnam.