The charge was made by the Irish Pharmacy Union (IPU) after the HSE wrote to individual pharmacists offering them a contract.
The IPU believes the terms offered under the contract will seriously undermine the rights of pharmacists and the viability of their business.
The union had urged the health authority not to make any changes to the current contract until the issue had been reviewed by an independent body proposed by the Minister for Health and Children, Mary Harney.
Pharmacists received a letter from the HSE on January 10 informing them that on March 1 the authority would be cutting payments for medicines dispensed under the community drug schemes by 8%.
Last November the HSE said it would delay the implementation of its proposal pending negotiations with the IPU.
According to the IPU however, the HSE declined to attend meetings with the IPU.
IPU president Michael Guckian said the proposals offered no benefit to pharmacies or patients.
“The HSE is showing contempt for due process and independent procedures by issuing this proposal,” he said.
“The executive committee will not allow our members to be discriminated and victimised by State institutions. We will ensure that pharmacists retain their right to representation, fair procedures and due process,” he said.