There are a number of features for EDI security. Almost all systems use password protection for access into the system. Most allow for multiple users and many provide access limitations for users. This limits the operations your employees perform based on your requirements. EDI also provides audit trails.
Authentication is another security feature.
This is the second level of your password. And finally, most systems use encryption in their transmissions. An individual cannot read the encrypted data. All these steps help ensure your data is secure. This lessens the chance that someone could link into your data at any specific point, as all points are randomized.