David Eckert said his employer, Alpha Funeral Service of Indianapolis, routinely loaned cadavers to Indiana University's School of Medicine, Courthouse News Service reported.
When three cadavers went missing, Eckert said he was ordered to "get this handled and taken care of" by his boss, owner Anthony Edwards.
Eckert said the only way he could do so was to create fake remains and false ID tags and misrepresent the identities, a Class D felony in Indiana.
In a lawsuit filed against Alpha Funeral Service, Eckert said he was forced to resign Oct. 16 after refusing the order.
In the suit, he said his boss had previously misrepresented the identities of cadavers with the compliance of the director of the Anatomical Education Program for Indiana University's School of Medicine.
Eckert's lawsuit seeks lost wages and punitive damages for wrongful discharge.
Notable deaths of 2014 [PHOTOS]