Simon Ledsham, head of central operations at Cancer Research, said the sales were of loss-making shops and that money raised would be spent on re-fitting existing shops and on improving ways of acquiring donated goods.
The leases being sold have an average eight years to run. With leases costing an average £20,000 a year, the charity expects to save around £1 million as well as making additional savings in managers' salaries and other overheads at the stores that are being closed.
The shops are spread around the UK and a third are in towns where Imperial Cancer Research Fund and Cancer Research Campaign had shops. Property company Corpra is handling the sales.
"We are not closing shops simply because there are dual sites, but because they are loss making,
said Ledsham, adding that in many other dual site towns both shops would remain open because they were profitable.
The merged charity has 675 shops. It has closed 20 so far this year and both charities had their own disposal programmes before the merger.
But he said that in general, the charity shop business was performing well, with sales up six per cent in the last financial year and indications that demand this Christmas would be strong.