The Association of School and College Leaders said it is concerned by high absence rates across England and urged the Government to increase investment in services for disadvantaged children most at risk of missing school.
Department for Education figures show that at least 3,014.56 pupils were absent from state-funded schools in Wigan in the last week of March, just before the Easter holidays.
That equated to 11.6 per cent of pupils from schools which responded to the survey that week – up from 7.1 in the week to February 10, before half term.
Nationally, 11.4 per cent of pupils were absent before the Easter holidays, up from 9.7 in February.
Pupils can be listed as absent for any reason, including general sickness, contracting Covid-19, isolating as a positive contact, and any other disciplinary issue or unexpected absence.
The latest figures do not specify what proportion of pupils were absent due to Covid-19.
In Wigan secondary schools, 15.4 per cent of pupils were absent, more than the 7.2 per cent in primary schools.
A further 12.3 per cent of pupils did not attend special schools in the area.
The National Association of Head Teachers has criticised the Government's approach to handling Covid-19 in schools, arguing it is attempting to "pretend the pandemic is over".
Paul Whiteman, general secretary of the NAHT, said: "The 'living with Covid plan' is increasingly looking like an 'ignoring Covid plan' when it comes to schools."
He warned that disruption may continue in the future, and that it is important no pupil is disadvantaged by it.
"We are not out of the woods yet," added Mr Whiteman.
The Department for Education said it is focused on increasing school attendance to ensure "every child gets the best possible education, no matter whey in the country they live."
The disruption caused in schools across England before Easter extended to staff, the ASCL and NAHT said.
Some 7.7 per cent of teachers and 8.4 per cent of teaching assistants were absent in Wigan in the week to March 31.
Geoff Barton, general secretary of the ASCL, said: "It is very clear that Covid is continuing to wreak havoc and it is hard for schools to operate under these conditions.
He added that pupils from vulnerable and disadvantaged backgrounds have been unfairly hit by the pandemic, and the high rate of absence is because they have become "disengaged from education".
Mr Barton urged the Government to increase investment in attendance and pastoral services to aid schools' efforts to support vulnerable children.
In Wigan, 12 per cent of children eligible for free school meals were absent from school before the Easter break.
A DfE spokesperson said it is pushing forward with plans to require schools to have an attendance policy that must meet national standards.
They added the department has also introduced attendance advisors to support local authorities and academy trusts and will continue to implement best practice among social workers, mental health practitioners and other health officials.