The figures emerged as the Scottish Government was accused of having a “tired and unambitious” plan to help students who missed out on schooling due to the pandemic.
Figures obtained by the Scottish Liberal Democrats show the percentage of primary school pupils missing at least half of their scheduled schooling had risen from 0.2 per cent to 1 per cent of all pupils. More than a quarter (25.4 per cent) were absent for more than 10 per cent of the year.
Pre-pandemic figures from 2018/19 state fewer than 15 per cent of pupils were absent for more than 10 per cent of their schooling.
This figure has also risen to almost half of pupils in secondary schools, with 49.6 per cent of secondary pupils missing at least 10 per cent of their schooling during the past academic year.
The number missing more than half has doubled from 2 per cent in 2018/19 to 4 per cent in 2020/21.
Willie Rennie, the party’s education spokesperson, said the impact of the virus on pupils meant increased absences as Covid-19 spread rapidly in school estates.
He said: “Teachers, parents and pupils did an incredible job learning as well as they could during the pandemic. However, what these figures show is that school absences increased dramatically as pupils were struck down by the virus or forced to repeatedly isolate.
"There is limited assistance to help young people's education bounce back from the pandemic.
“Every minute in school is precious for young minds and the loss of so much time is such a loss of opportunity to grow.
"The SNP' s education recovery plan is tired and unambitious. The poverty-related attainment gap is as wide as ever and the SNP have run out of ideas on how to close it.
“The Scottish Liberal Democrats have set out plans for bounce back support in schools, including more teachers and assistants to cut class sizes, guaranteed outdoor learning and a guided programme of additional support for senior pupils. That's the kind of ambitious plan that the SNP Government should learn from."
Scotland’s largest education union, the EIS, said pupils missing school leads to “challenges” for pupils and teachers alike, and called for better measures to avoid a repeat this winter.
A spokesperson for the union said: “Clearly, the winter months can increase the risk of pupils missing school as a result of illness. The normal winter viruses, coupled with still high rates of Covid infection, can lead to significant numbers of young people being absent from school.
"This creates challenges for pupils and teachers alike, with interruptions to young people’s education when they are off ill.
"While some level of sickness absence is always expected, particularly during the winter months, this again highlights the need for continuing mitigations in schools to minimise the risk of viral spread – both to protect the health of pupils and staff and, also, to reduce the impact on young people’s education.”
Responding, education secretary Shirley-Anne Somerville said millions in funding had been pledged to help close the attainment gap and tackle the disruption from Covid.
She said: “We have invested almost £500m over 2020/21 and 2021/22 to help tackle education disruption caused by Covid. That includes £240m to support local authorities to support the recruitment of more than 2,200 additional teachers and over 200 support staff in 2020/21.
“Recognising that the impacts of Covid will have fallen most heavily on those who are already most disadvantaged, our refreshed Scottish Attainment Challenge – backed by investment of £1 billion in this Parliament – empowers schools and local councils to drive education recovery and accelerate progress in tackling the poverty-related attainment gap.”