CAN INDIAN COMPANY SUPPLY GOODS IN USD TO OTHER INDIAN COMPANY

Both Companies are located in India

While filling , GST return on GSTN portal , you Can not report any other Currency , both in GSTR1 and GSTR3B , I think its by default  its Indian Currency , please confirm.

This is why. Government has formed rules and laws. Most of the time, people are not obey or follow it. They want to write a new laws.

Best of luck.

Your wish may come true in future.