Professor Dame Sally Davies released her annual report for 2014 - which for the first time focuses on the health of England's female population.
She said action is needed to "empower women and their families to live healthier lives", warning that obesity could impact down the generations.
"I'm calling on the Government to elevate obesity to a national risk," Dame Sally said.
The national risk register of civil emergencies lists priority threats to the country including terror and cyber attacks and natural hazards such as flu pandemics.
"Action is required across all of society to prevent obesity and its associated problems from shortening women's lives and affecting their quality of life," she said.
"We need to address the educational and environmental factors that cause obesity and empower women and their families to live healthier lives."
The report revealed that in 2013, more than half (54%) of women aged 34 to 44 and almost two-thirds of women (62%) aged 45 to 54 were classified as overweight or obese.
Dr David Richmond, president of the Royal College of Obstetricians and Gynaecologists (RCOG), said: "Present lifestyle factors such as maternal obesity, poor diet and nutrition, lack of physical activity, high levels of alcohol consumption, smoking and poor sexual health are the ticking time bomb that can dramatically impact upon a woman's fertility and increase the risk of pregnancy complications ..."
The report also aims to "break the taboo" over health problems such as post-natal incontinence or the menopause.
"Problems 'below the waist' are not generally seen as attractive topics for public discussion, and women are often reluctant to seek help for common disabling conditions," Dame Sally added.
"This needs to end - women should never suffer in silence."
It also called for a "national audit of ovarian cancer" to boost survival rates.
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