The Scottish Conservative leader demanded answers after thousands in Tayside and Fife struggled to book appointments this month.
It saw NHS Fife chief executive Carol Potter pledge staff would now review how things went wrong, while the health board have also apologised.
The problems saw hundreds turned away for flu jabs due to what NHS Grampian described as “logistical problems” with the transportation of the vaccine.
Scottish Conservative leader Douglas Ross said: “The situation up and down Scotland relating to the administering of the flu vaccine is fast becoming a national scandal.
“The SNP’s failure to address issues early in the process is causing chaos and fear across Scotland as we head towards winter.
“My sympathies go out to patients and the NHS staff who are facing the brunt of the SNPs mismanagement.
“From the forever engaged flu line to having no stock – the situation is a shambles and a disgrace.”Mr Ross demanded answers, and urged the Scottish Government to urgently rethink the rollout.He continued: “These endless problems are causing distress and alarm across Scotland and must be addressed with the utmost urgency as another challenging period approaches.
“Our most vulnerable are continuing to be frozen out by the sheer mismanagement shown by the SNP on this matter towards our NHS staff and services they provide.”
It comes in the first year that Scotland’s 14 health boards have been handed control of delivering the programme instead of GP practices.
The first minister had previously claimed the concerns were being addressed, insisting the Scottish Government was working closely with the health boards.
She said: “The absolute priority, which everybody takes very seriously, is to get everybody who is eligible vaccinated as quickly as possible.”
Earlier this week Mr Ross accused Nicola Sturgeon of playing "constitutional games" while businesses and jobs are on the line.
The Scottish Conservatives leader accused the First Minister of failing to listen to small business owners amid claims they were "shut out" of lockdown planning.
The Moray MP insisted Scotland can "build back stronger" after the virus, and urged Ms Sturgeon to act now to save the economy.