But the Opposition felt pharmacists had no choice and had caved in simply to secure their funding.
Labour health spokeswoman Maryann Street said: "The change that this contract involves, and the haste with which it has been rushed through, threatens the livelihoods of many pharmacists and the care they can deliver as health professionals."
She said there was significant anxiety about patient safety and the survival of rural pharmacies.
Some pharmacists felt they would be forced to rush patient consultations in order to keep revenue flowing in.
Pharmacy Guild executive chair Karen Crisp said concern had been expressed about the complexity of the new funding scheme, but the majority of businesses were happy with it.
She said most pharmacies would earn the same amount of revenue under the new agreement.
The majority of patients would be unaffected by the changes.
People who frequently went to the pharmacy to get medicine might be able to collect their products all at once. Patients who were frail or had long-term conditions would have more hands-on support from pharmacists to help them manage their medicine.
Mrs Crisp said pharmacists had been under-used in primary care, and the new agreement recognised their expert skills.