Department for Education figures show "wilful and repeated transgression of protective measures" was a reason behind 364 exclusions from schools in Doncaster in the 2020-21 academic year – 363 of which were temporary exclusions and one permanent.
Of these, 356 were in secondary schools and eight in primary schools.
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It means there were 77 exclusions for breaches of Covid measures for every 10,000 pupils in Doncaster – one of the highest rates in the country.
Children across England were excluded 12,965 times for reasons including non-compliance with social distancing, causing distress such as by purposefully coughing near to others, or any other deliberate breach of a school's public health measures.
Schools were able to list multiple reasons for each exclusion for the first time last year.
Julie McCulloch, director of policy at the Association of School and College Leaders, said schools worked very hard to keep pupils and staff safe during the pandemic, and it is not unreasonable that young people should be expected to comply with these measures.
However, Stephen Morgan MP, Labour’s shadow schools minister, said: “The Conservatives have created deep divides in school exclusions, with the lack of clear guidance, especially during the pandemic, threatening children’s futures and failing communities.
“The Government’s own independent review highlights the need to tackle exclusions and ensure children are supported in order to improve life chances.
“No parent wants to see their child excluded from school but once again the Conservatives have treated our children and their future opportunities as an afterthought.”
In Doncaster, there were a total of 5,849 exclusions (5,826 temporary and 23 permanent) for all reasons last year – down from 6,344 in 2019-20.
Figures for the most recent academic year include a period in spring 2021 when Covid-19 restrictions meant that only key worker and vulnerable children were attending school in person, with others being educated remotely.
Of the 16 possible reasons for exclusion, public health was the fourth most frequent.
The most common reasons were for persistent disruptive behaviour (56%), verbal abuse or threatening behaviour towards an adult (15%) and physical assault against a pupil (10%).
The National Association of Head Teachers said schools following guidance were sometimes forced to suspend students in cases of persistent rule breaking and unsafe behaviour, with school leaders making tough decisions to keep everyone safe.
Paul Whiteman, general secretary of the union, said exclusions are always a last resort – and have fallen to an all-time low across England – but should not mean the end of the road for pupils affected.
He added: "Unfortunately cuts to health and social care services mean that the safety net for excluded young people has too many holes in it.
"This is something that the Government should address urgently.”
A Department for Education spokeswoman said permanent exclusions are a rare but necessary way of managing behaviour – but should not mean exclusion from education.