The Irish Haemophilia Society (IHS) and Transfusion Positive said they were disappointed with the ruling and were concerned about the impact on more than 100 of their members who had hoped to have their awards increased.
IHS administrator, Margaret Dunne, said the decision left the law fundamentally unjust and called on Micheál Martin to introduce an amendment to provide redress for affected patients.
"The State has admitted liability for the injury to these people and the compensation tribunal was set up to provide fair and just awards but now a technicality is being used to limit what is fair and just," she said.
The Supreme Court's decision affects victims who accepted awards from the Hepatitis C Compensation Tribunal but discovered later the payments did not adequately reflect their suffering.
Under the legislation enacted to set up the tribunal in 1997, claimants have a month to decide whether to accept or reject the compensation and if they reject it in this time, they can appeal to the High Court to award them an increased amount.
Initial compensation payments have varied enormously, averaging out at around €210,000, but the trend has been for the High Court to substantially increase awards.
Yesterday's ruling centred on a test case by an unnamed member of the IHS who signed off on a £125,000 (€159,000) award in 1997 without taking the month to consider his options and later found it was not sufficient.
The High Court ruled last year that he was not time-barred from appealing the amount but this decision was appealed by the minister for health and the compensation tribunal, resulting in yesterday's decision which was unanimous among the five judges.
At least 70 IHS members similarly accepted initial awards, believing them to be sufficient, but later found their health deteriorating to a far more serious extent than they anticipated. Ms Dunne said some were now facing liver transplants.
Transfusion Positive chairperson, Maura Long, said quite a few of that group's members were also affected by the decision.
"There is not just physical damage there is the psychological effect and that is not always evident in the early days. There is also the knock-on effect one person is infected but an entire family is affected," she said.
Positive Action co-ordinator, Mary O'Connor, welcomed the Supreme Court's clarification of the question but said the decision would cause disappointment.
"Some people were under such pressure and such stress after their diagnosis that even though they might have been advised to reconsider the compensation tribunal payment, they accepted it because they just felt they could not go any further.
"It was only in the cold light of day they realised they should have pushed on for more," said Ms O'Connor.
Mr Martin said he had no plans to change the legislation.