Medical incident reports (MIRs) are documents that record what happened in a medical incident. A typical MIR consists of two sections: a structured categorical part and an unstructured text part. Most texts in MIRs describe what medication was intended to be given and what was actually given, because what happened in an incident is largely due to discrepancies between intended and actual medications. Recognizing the intention of clinicians and the factuality of medication is essential to understand the causes of medical incidents and avoid similar incidents in the future. Therefore, we are developing an MIR corpus with annotation of intention and factuality as well as of medication entities and their relations. In this paper, we present our annotation scheme with respect to the definition of medication entities that we take into account, the method to annotate the relations between entities, and the details of the intention and factuality annotation. We then report the annotated corpus consisting of 349 Japanese medical incident reports.