An email sent to all GPs in the Edinburgh area said the issues were not expected to be ironed out until January 25, delaying the rollout of the jab to some elderly patients.
It also said mass vaccination centres were not expected to be operational until February 15 due to a potential delay in the creation of a national booking system for jabs.
However, the Scottish Government insisted last night the booking system would launch later this month and the information sent to GPs contained “inaccuracies”.
The email, sent on January 8 by the Edinburgh Health and Social Care Partnership (EHSCP), also confirmed the Edinburgh International Conference Centre will be the main venue in the capital for mass vaccinations.
It said officials were also working on an agreement to use the Royal Highland Centre on the western outskirts of the city, as well as Queen Margaret University in Musselburgh.
The email, entitled “EDI Friday 8th January SITREP”, also suggested the key problem faced by GPs delivering the vaccine is obtaining reliable supplies.
“As everyone is aware, this is what is currently limiting our endeavours,” the email read.
“Our best understanding is that the supply will increase and become more reliable and proportionate to practice numbers from week beginning 25th January, so a couple more weeks of frustration during which some 80+ patients will be getting the vaccination whilst others have to wait longer.”
It also suggested that mass vaccination centres might not become operational until the middle of February, partly due to delays with creating a national booking system for patients.
“We were planning on starting both mass and local clinics on Monday 1st February, but there may be delay in the delivery of the national booking system, which might knock this back to 15th February (tbc),” the email read.
“If we are likely to have an established vaccine supply by early February, then we are considering how we might offer appointments for some or all of the 75-79 [year old] cohort, in advance of having the national booking system available.”
Figures published on Tuesday showed 175,942 people in Scotland have received the first dose of the Covid vaccination so far, an increase of 12,565 in the space of 24 hours.
A Scottish Government spokesman said there were “inaccuracies” in the information sent to GPs and that EHSCP would be issuing a correction.
“The vaccination programme is functioning well across Scotland – and it is entirely incorrect to claim otherwise,” the spokesman said.
“The national scheduling system will be ready this month and we anticipate no delay to appointments during the rollout.
“The Health Secretary will provide a detailed update to Parliament this week on progress to date, including on vaccine supply, delivery methods, locations and expansion of the workforce to support the programme.”
An EHSCP spokeswoman said: “The Covid vaccination programme is moving at pace and information shared internally last week is already out of date.
“GP practices in Lothian are doing a magnificent job of rolling out the vaccination programme to the over 80s and we expect supplies of vaccine to increase throughout the remainder of the month.”