The apology came after concerns had been raised over some patients not receiving their letters in time to attend their appointments.
In a statement the Scottish Government said that the “issue” meant that letters distributed “to a number of patients” across Scotland had been delayed, but did not reveal the exact number.
A Scottish Government spokeswoman said: “We have identified an issue with our appointment system which has delayed appointment notifications being distributed to a number of patients across Scotland.
“Appointment letters will be issued this week and we believe that patients should still receive four days’ notice of their scheduled appointment.
“We appreciate that this may not be enough notice for everyone affected. The appointment letter contains details on how to view or amend your appointment online.
“We apologise for any inconvenience caused but would urge everyone to attend their scheduled appointment where possible to allow us to continue to vaccinate at pace.”
If you receive a letter and need to reschedule you can call the vaccination helpline on 0800 030 8013.
The admission from the government comes after reports that as many as half of all vaccination appointments booked to take place at the Hydro in Glasgow were missed last weekend.
NHS Greater Glasgow and Clyde is investigating the reasons behind why many people scheduled for a Covid-19 vaccine over the weekend apparently failed to show.
Scenes similar to those seen in Glasgow were reported in Edinburgh last weekend when a quarter of all patients failed to turn up to their scheduled appointments at the city’s largest vaccination centre, the Royal Highland Centre.
NHS Lothian did not speculate the reasons as to why this may be but has continued to urge those who cannot attend their appointments to inform the centre in advance.
It is understood that the government is working with health boards across the country on the level of missed appointments to discover whether the issue is localised or more widespread.