In response to a question from Craig Hoy, MSP for South Scotland, during First Minister’s Questions on Thursday, Mr Swinney said the issues in the NHS Lothian area “should be resolved shortly”.
Mr Hoy said that one constituent, Norma from Dirleton, had already received her booster, but had received four letters inviting her to appointments, which she had been unable to cancel.
Her 88-year-old neighbour had meanwhile received no appointment letter and had tried to attend a mobile vaccination bus to get her jag, but was forced to leave due to the length of the queues.
He asked: “Will the Deputy First Minister urgently look into the ongoing problems in the vaccine booster scheme across the Lothians?”
Mr Swinney said: “The booster programme in general has been rolled out very, very effectively and the booster programme is being rolled out across the country very successfully indeed.
"Scotland is the highest performing part of the United Kingdom in relation to the rolling out of the booster programme.
"However, there have been a number of issues in NHS Lothian in connection with the appointment system, with which we are familiar.
"We are obviously in discussion with NHS Lothian and our officials met with the chief executive agents within Lothian this week to discuss these very practical issues that Mr Hoy raises with me.
"I am sorry for the inconvenience that this constituent has experienced, they should not have experienced that.”