The Indian flag on the official blazers of the athletes had no white strip in the middle and country's name was also not printed on the back.
The Internationanl Paralympic Committee objected to it and rejected the kit, jeopardising Indian athletes' particpation in the ceremony.
"The Chef-de-Mission of the Indian contingent in Rio has informed that inspection of uniforms/kits of the participating countries is a routine affair in such mega events. This was done in the case of Paralympics, 2016 as well. After the inspection, IPC made some suggestions to India as well as many other countries. The issues raised in respect of the ceremonial kit of the Indian Contingent have since been resolved," a Ministry release said.
India have sent their largest ever contingent for the Rio Paralympics as a total of 19 athletes will vie for honours.