The duo was on bail from October 29
The Chittagong Metropolitan Magistrate Khairul Amin passed the order after the investigation officer of the case sought 10-day remand for each of them on Monday.
The commission employees are Satyasundor Dey and Sagar Chowdhury. Both of them were involved with NID preparing project in Dhaka.
On Sunday, the duo surrendered before the court and prayed for bail. However, the court rejected the bail prayer and ordered to send them to jail.
On October 29, the duo secured bail from the High Court for a four-week period.
Counter-Terrorism Unit of Chittagong Metropolitan Police (CMP) is investigating the case.
Counter-Terrorism Unit Inspector Rajesh Barua told Dhaka Tribune that they prayed for a 10-day remand but the court granted seven-day remand for each.
On September 16, the police arrested three people including an Election Commission staff Joynal Abedin for helping Rohingyas get NIDs.
Later, Joynal Abedin confessed to the police that Satyasundor and Sagar were also involved with the NID scam.