Yes, as long as you’re not discriminating based on protected classes or characteristics, you can conduct reference checks for certain roles but not others. For example, you may decide that supervisory roles or positions with access to sensitive information warrant this additional step during the hiring process. As with any reference check, don’t forget to get the candidate’s permission first.
That said, some employers like to have consistent practices across the board to reduce the risk of a discrimination claim. Employees can file claims based simply on the appearance of discrimination, and employers may be held liable even if they didn’t intend to discriminate. In this case, doing (or not doing) reference checks for all roles would be the most risk-averse approach.
If you would like to check references only for certain employee groups, you should consider whether your policies and practices are disproportionately affecting employees who share a protected characteristic (race, sex, age over 40, etc.). If candidates who were rejected after a reference check were all or mostly the same gender, for instance, you’d want to be sure that the reference checks were both a business necessity and that there was no other policy you could implement that would have less of an impact on the protected group.