The Irish Pharmaceutical Union had said a number of summons were served on pharmacists in Dublin tonight by the Competition Authority and gardaí.
The IPU said its members were very anxious to engage with the Health Service Executive to find a resolution to the dispute.
In a statement on its website, the Competition Authority said it had begun an investigation into the withdrawal of 140 pharmacies from the HSE's methadone scheme this week.
Section 4 of the Competition Act bans any agreements, which could lead to the prevention, restriction or distortion of competition.
The Registrar of the Pharmaceutical Society of Ireland Dr Ambrose McLoughlin has formally advised all 140 pharmacists to stop their action immediately and return to providing care.
Dr Ambrose expects them to comply with his wishes immediately, but warns that if they do not he will take further action.
He also says that he believes the overwhelming mass of pharmacists will realise this action is a step to far, as this is an industry that cares about its patients.
Earlier today, the Taoiseach Bertie Ahern has told pharmacists to stop involving recovering drug addicts in their dispute over fees with the Health Service Executive.
He said there was no justification for what they are doing and said they should stop immediately. Mr Ahern said the dispute had nothing to do with addicts and it was totally wrong to involve them in it.
Labour leader Eamon Gilmore raised the issue by asking how the Competition Act was blocking negotiations with the pharmacists' union when it had not stopped talks on fees with the Bar Council, the Law Society, the Dental Association and Veterinary Ireland.
More than 140 Dublin pharmacies pulled out of the HSE's methadone protocol last Monday in a row over a new drug payment structure.
The head of the HSE pharmaceutical office urged pharmacists to resume services to methadone patients, saying he would do anything to resolve the situation. However, Professor Kamal Sabra said the HSE could not negotiate fees with the IPU as this would be in breach of competition law.
The HSE says the new arrangements will slash an estimated €100m off the State's drugs bill next year, but pharmacists say it will result in them having to dispense medicine to public patients at a loss and put their businesses at risk.
