The organisation representing the pharmaceutical industry has claimed that patients are not getting access to new medicines.
It also claims that the HSE is not funding medicines that have been independently deemed as cost-effective.
Speaking on RTÉ's News at One, President of the Irish Pharmaceutical Healthcare Association David Gallagher said that over the last six to eight months, effectively no new innovative medicines have been added to the drug reimbursement scheme.
He said that there were a good eight or ten medicines that have gone through the licensing process and a health technology assessment that have been proven to be cost effective.
"Ordinarily there would be reimbursement, but since September they haven't been added to the reimbursement scheme," said Mr Gallagher.
The IPHA said patients are not getting access to new medicines for multiple sclerosis, heart conditions, bipolar disorder and Hepatitis C, while there are restrictions on others.
The Department of Health today agreed to an interim proposal from the IPHA, which offers drug price reductions in certain areas and will allow for full scale talks to try and agree a new long-term deal on medicines.
The department said the interim agreement will save €20m in a full year, which will allow for needed medicines to be made available to patients.
The previous agreement which lasted over five years expired at the start of March and discussions have been under way since then to replace it.
The expired agreement provided for new medicines to be made available within 40 days of a positive reimbursement decision.
The HSE has set a target of €112m in drug savings this year.
It said that at any time, a number of drugs are at various stages of the decision-making process for reimbursement.
Health Service Executive negotiates
The HSE said it negotiates directly with drug companies on price to try and find a sustainable way to make new drugs available for public use.
The Department of Health is also planning legislation to allow for new price controls and substitution of certain medicines with cheaper generic equivalents.
Among the recently approved medicines that manufactures say are not being funded are Brilique, for acute coronary syndromes; Gilenya, for multiple sclerosis and Sycrest, for bipolar disorder.
Two drugs for Hepatitis C, Incivo and Victrelis, have been approved for reimbursement and a decision is due on what budget they will be funded by.
In the case of another drug, Pradaxa, for stroke prevention after hip or knee replacement, any patient currently on it can remain on it but usually just for a month.
The HSE said that no new patients should be prescribed Pradaxa for the heart condition atrial fibrillation until an assessment is completed and the HSE assesses whether it has the money for the long-term treatment of patients.