Public Health Scotland (PHS) released statistics on Tuesday showing the spending in 2020/21 increased by 5.2% in real terms compared to the previous year.
The statistics do not cover spending by agencies such as NHS24, Healthcare Improvement Scotland and National Services Scotland.
Pressures from the pandemic meant it was not possible to collect the normal level of detail on NHS spending, the report said.
Instead, it presented a “high-level costs summary” covering the 14 territorial health boards, the State Hospital at Carstairs and the Golden Jubilee National Hospital.
Of the additional expenditure, £615 million (39%) went to hospital services and £843 million (54%) on community services.
The PHS report said: “This additional expenditure includes additional expenditure incurred by NHS boards due to the coronavirus (Covid-19) pandemic.
“Although not quantified explicitly, this will be influenced by the cost of additional services such as Test & Protect and the Covid-19 vaccine programme as well as the expenditure associated with additional infection control measures such as the cost of PPE (Personal Protective Equipment).
“This has contributed to a larger year-on-year increase, in both cash and real terms, than in previous years.”