In 2018 the Therapeutic Goods Administration's Complaints Resolution Panel upheld a complaint about ads by this company on the grounds that they breached advertising codes. The ads were subsequently withdrawn.

In December 2016 Chemist Warehouse was ordered to back-pay more than $3.5 million for mandatory online training its workers did in their own time. Some 5976 employees, making up almost two-thirds of the retail pharmacy chain's workforce, have been paid back an average of about $600 for the training following an extensive Fair Work Ombudsman audit.

This company has been criticised for offensive advertising. In 2015 and 2020 the Advertising Standards Bureau upheld complaints about ads by this company on the grounds that they breached advertising codes. The ads were subsequently discontinued or modified.