"The government has ordered an investigation. If the NGO is found responsible for any wrongdoing, the government will take stern against perpetrators," Health and Education Minister Tapan Chakraborty said.
Congress leader Birajit Sinha had raised the issue in September.
The NGO, in north Tripura's Kailashahar area, had allegedly enrolled around 600 housewives as sex workers and siphoned lakhs of rupees, Sinha told the House.
He said that housewives, tea workers and women belonging to minority groups had been enrolled as sex workers without their knowledge. The NGO collected blood samples on the plea of malaria finding exercise.
The NGO authority has denied the allegation.