The Dumbarton MSP is seeking clarity on the level of vaccines which are wasted and stepped up demands for national guidance on who should be on reserve lists to minimise this.
It comes as the Scottish Government sets out a new campaign to encourage take-up of the vaccine in Scotland.
Ms Baillie raised concerns over vaccine wastage at First Minister Questions yesterday.
The letter to Ms Sturgeon states: “Medical staff across the country are doing an incredible job under difficult circumstances to ensure that this rollout is a success and we are all thankful for their work.
"As you agreed, it is of critical importance that as much of the vaccine as possible finds its way into people’s arms.”
Ms Sturgeon said yesterday that wastage levels stood at about 1per cent, but Ms Baillie pointed reports suggesting it was 1.8 per cent, indicating that this could mean "thousands of doses" are effectively lost across the population.
The interim Labour chief also called for national guidance to be issued to "all vaccinators to ensure that they have a reserve list of priority and high-risk patients so that doses are not wasted".
Recent BMA calls for the Pfizer vaccine to be available for uses as a second dose for NHS staff to avoid wastage should be looked at, according to Ms Baillie, who also wants weekly vaccination wastage statistics published.
Ms Sturgeon said yesterday that any major vaccination programme will see some wastage through "human error", with inevitable occasions when vials are dropped and break, resulting in vaccine loss or having a syringe prepared when someone doesn't turn up for an appointment.
"That's just unavoidable to some extent but the effort is to minimise it".
It comes as a new campaign is launched today aimed at encouraging people to get vaccinated for COVID-19 as soon as they are eligible launches.
The ‘Roll your sleeves up’ campaign will emphasise the importance of the vaccine and its safety, as well as the prioritisation list set out by Joint Committee on Vaccination and Immunisation (JCVI) to ensure those most at risk are vaccinated first.
Health Secretary Jeane Freeman said: "Vaccination offers us greater protection against COVID-19 and it offers us hope that this year will be a brighter one.
"It is another vital tool in our work to suppress the virus, but other measures including testing, and lockdown restrictions remain absolutely essential to suppress COVID to the lowest possible level in Scotland."
Vaccination will be offered to 4.5 million people in Scotland and is currently underway for residents of care homes for older people and their carers, frontline health and social care workers, and those aged 80 years and over.
Interim Deputy Chief Medical Officer Dr Dave Caesar said: “No matter which vaccine you receive, each has passed a rigorous three-phase testing process, reviewed by independent regulatory and advisory bodies to ensure it is safe and effective. Your local NHS health board will be in touch with you to arrange your vaccination appointment when you are eligible, and I encourage everyone to get vaccinated as soon as they are eligible to do so.”