The area had 744 new cases per 100,000 people in the seven days up to and including 29 September. Only Kettering had a higher rate in England.
A month ago, the rate in Rugby was half that.
Almost half of all new cases are in schools and some head teachers have reintroduced face masks.
Masks stopped being compulsory in secondary schools from 17 May, but the Department for Education has said masks can be temporarily brought in for areas with higher Covid rates.
Siobhan Evans who runs Ashlawn School said the measures were helping to reduce cases.
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