Fewer than half of those sent bowel screening kits completed them and only three quarters of women had cervical screening tests.
Of 374,907 people sent bowel screening kits between April 2011 and March 2013, 185,932 kits were completed and returned for analysis, an uptake of just 49.6%.
The lowest uptake was among people with a learning disability at 28% and men aged 50-54 at 38%.
Residents living in the most deprived areas were least likely to take the test at 39.6%, compared with 60% in more affluent areas including East Renfrewshire.
Bowel cancer is the third most common cancer in Scotland after lung and breast cancer.
Each year, almost 4,000 people are diagnosed with the disease.
In 2012 the disease claimed the lives of 356 people in the Greater Glasgow area.
All men and women in Scotland between the ages of 50 and 74 are invited for screening every two years.
The data also shows more women than men are taking the test at 52% compared to 47%.
Dr Emilia Crighton, Consultant in Public Health Medicine at NHSGGC said: "I urge everyone who receives an invitation letter and test kit to take part in the potentially life-saving screening programme.
"Early detection of colorectal cancers through screening will result in more effective treatment and improves survival rates."
In Glasgow, only 75.1% of women who were invited to go for cervical screening sessions, or smear tests, ttended appointments last year, but in some areas of the city these rates fell as low as 65.7%.
Linda de Caestecker, Director of Public Health at NHS Greater Glasgow and Clyde, said: "Uptake for cervical screening is not in significant decline, but the fact we're not increasing it is a concern.
"The lowest uptake is in our young women."
Just over half (57%) of eligible 21 to 24-year-olds were screened last year - a decrease of nearly 3% compared to the previous year.
The NHSGGC now plan to launch a campaign aimed mainly at young women, to try and encourage them to go for the vital smear tests which can detect early signs of cervical cancer.
Dr Crighton, said: "We have been trying to gain insights into why women do not take up the screening, so we spent nearly two years developing a focus group and working with practice nurses to develop the campaign."
Videos and posters focusing on some of the barriers which may stop people from having smear tests, including fear and embarrassment, will play a key role in the drive.
In Inverclyde, 78% of women took up the offer of screening, while in East Renfrewshire and East Dunbartonshire more than 80% of women invited to appointments attended.