Lloyds Pharmacy has confirmed its working with the HSE in relation to its dispensing services.
The company - which has 93 outlets across Ireland - says it strongly refutes allegations relating to its phased dispensing service.
The HSE says its investigation relates to both current and historic claims and that the inquiries are open-ended.
In a statement Lloyds says the company adheres fully to HSE guidelines and has accused the Health Service Executive of changing how it interprets these.
