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There are 113 cancers detected per 100,000 people in South Canterbury.
That compares to a national average of 65.7.
National Bowel Screening Programme clinical director Dr Susan Parry said bowel cancer is often a symptomless disease, so screening is very important.
"The home testing kit is designed to pick up tiny traces of blood in a bowel motion and to catch cancers before they become advanced and more difficult to treat," Dr Parry said in a statement.
The scheme will be offered to people aged between 60 to 74 in Timaru and surrounding districts.
Dr Parry said around half of South Canterbury's residents fall into this age group which means they will be eligible for free bowel screening.
Over the next two years, around 12,000 people will be invited to complete a home testing kit that can detect treatable early signs of the disease.
The National Bowel Screening Programme is now available in 12 district health boards with Canterbury DHB the next to launch.
The programme is expected to be implemented nationwide by the end of 2021.