Schools across England reopened to all year groups from September, with students sent home in bubbles to self-isolate when coronavirus cases were detected.
Pupils across Portsmouth missed the equivalent of 104,793 days of in-person education between September and December for this reason, Department for Education figures show.
That was an absence rate of 6.4 per cent, and equivalent to roughly four days per pupil.
While pupils at schools covered by Hampshire County Council missed the equivalent of 433,540 days during the same period.
The figures include state-funded primary, secondary and special schools in the area.
Schools recorded general absence – including when authorised and unauthorised – separately, although this could include a child being ill due to having Covid-19
The absence rate in Portsmouth for the autumn term was around 5.1 per cent, which was similar to 5.2 per cent the previous year.
In Hampshire it was 3.9 per cent – among the lowest in England – and equivalent to roughly three days per pupil.
By comparison, England’s overall absence rate for the autumn term was 4.7 per cent – broadly in line with 4.9 per cent a year earlier.
But a further seven per cent of in-person teaching was missed because of self-isolation or shielding due to Covid-19 – amounting to 33 million days, or five days per pupil.
Geoff Barton, general secretary of the Association of School and College Leaders, said the figures show the autumn term was ‘an extremely turbulent period’ for pupils.
‘This difficult situation was compounded by significant problems early in the term, obtaining Covid tests for pupils and staff and in obtaining public health support in handling positive cases,’ he said.
‘The government’s refusal to give schools any flexibility to finish in-school teaching early before Christmas, which was accompanied by threats of legal action, made matters even worse.’
Schools were ‘badly let down’ by government leadership during the autumn term, Mr Barton added, including by the ‘painfully slow’ rollout of laptops for disadvantaged children that made remote education harder.
A Department for Education spokesman said schools went to great lengths over the autumn term to become Covid-secure.
He added: ‘Where students did have to self-isolate, schools provided high-quality remote education, supported by an unparalleled government rollout of laptops and tablets for eligible children.
‘It is positive to see underlying absence slightly decreased compared with previous years, reflecting schools’ efforts to keep their students engaged throughout an incredibly challenging year.’