Absenteeism from colds and flu costs UK businesses £1.1billion each year, according to Co-operative estimates.
The staff, who work in more than 4,500 locations across the UK, will be offered the jab either at 42 workplace clinics or via 400 of The Co-operative Pharmacy's branches, which are also offering the vaccination to consumers and other businesses for £11.
The Co-operative estimates it will save at least £1 million a year if 75% of its workforce takes up the offer.
It has been argued that a swine flu outbreak and the impact of workers being unable to go to work because of illness could affect overall UK GDP by 3%
Wayne Lee, director of employee relations and reward at The Co-operative, said: "Reducing the costs and impact on business efficiency from workplace absenteeism is particularly important in these difficult economic times. Our leading approach to offer flu vaccinations to our staff makes business sense while improving the welfare of our employees."
The inoculation, supplied by Novartis Vaccines, contains the H1N1 (swine flu) strain in line with World Health Organisation recommendations and has been ordered from stocks outside those allocated for the NHS.
The Co-operative Pharmacy also offers an on-site vaccination service to businesses with more than 100 employees.
