NHS Grampian has vowed to resolve the issues affecting its flu vaccine programme within the next ten days.
As well as running out of vaccine at a number of centres, would-be patients also received their letters on the day or after their scheduled appointment.
The health board said it was working to overcome the issues affecting the system and offered reassurance that all those eligible will receive their flu jab.
Additional phone lines will be put in place from Tuesday, with extra staff being brought in to answer calls and emails over appointment concerns.
Adam Coldwells, NHS Grampian’s deputy chief executive, said: “Work continued at pace over the weekend to resolve these issues and to deliver the vaccine.
“In the next ten days we expect to be ahead in terms of getting letters delivered and people should be receiving these in good time.
“Unfortunately it is likely in next few days some people may receive their letters either on the day or after their appointment. These people do not need to worry, they should call the helpline and we will book them back in.”
NHS Grampian said tens of thousands of people in the region have already had their jab.
The helpline – set up to assist those who can’t attend their given appointment – has been inundated with calls. However, many were from people yet to receive their appointment and from others raising concerns about the change in the system.
Mr Coldwells said: “We need people to be patient with us.
“Everyone will receive their appointment letter in the next three to four weeks. Please do not call the helpline if you haven’t received your letter. We will get to you.”
Those who have missed their appointment will be given another. And as the flu programme runs for a number of weeks, letters are being sent out in batches and not at the same time.
Flu vaccine clinics are being held in schools during the October holidays and there will be further clinics into mid-December to ensure all priority groups are covered.
Mr Coldwells added: “No one will miss out on their vaccine as a result of these issues – that’s very important to remember.
“We’ve apologised for the issues and we’re working extremely hard to get back on track. It’s the first time we have delivered the vaccine like this and there has absolutely been teething issues and a learning curve.
“We’d logistical problems getting the vaccine to some venues and, again, that’s something we’re working to avoid a repeat of.”
Pregnant women living in Aberdeenshire and Moray will be offered their flu vaccination from their community midwife.
In Aberdeen, women will be invited to attend a vaccination appointment at Aberdeen Maternity Hospital prior to their 12 and 20-week scans. The immunisation team will make direct contact with those women.
Appointments are currently being issued for those aged between two and five.