Kimia Farma, which is headquartered in the capital Jakarta, has since fired the staff involved and promised to tighten internal controls.
This week, two lawyers who frequently flew via Kualanamu airport in recent months, said they were planning to sue Kimia Farma, the South China Morning Post reports.
In a collective lawsuit, they hope to get 1 billion rupiah for each passenger who has been affected by the scheme.
Earlier this week, Indonesian authorities said they had identified two cases of the new Covid variant first seen in India.
Last month, Jakarta stopped issuing visas for foreigners who had been in India in the previous 14 days.
The Muslim-majority nation has also banned domestic travel at the end of Ramadan this month, a period which traditionally sees people travelling across the country to visit relatives, and introduced heightened restrictions for other dates.
Indonesia has seen one of the worst Covid outbreaks in Asia, and overall has recorded about 1.7m positive cases and more than 46,000 deaths linked to the pandemic.