A third of the mothers had not worked since the birth of their child, but the mothers who were employed were spending an average of 21 hours a week at work.
They took into account factors likely to influence the results, such as the mothers' level of education and socioeconomic circumstances.
They found that five-year-olds whose mothers worked part-time or full-time were more likely to primarily consume sweetened drinks between meals.
They used their computers or watched television for at least two hours a day compared to the children of "stay at home" mothers who spent less than two hours on these activities.
They were also more likely to be driven to school compared to the children of "stay at home" mothers who tended to walk or cycle.
The children whose mothers had a flexible working pattern did have healthier lifestyles but when other factors were taken into account the researchers said there was little evidence that these children behaved more healthily.
Debbie Bird: "'Being a working mum is very challenging"
Professor Catherine Law, who led the study, said they had not looked at fathers in this study because fathers employment levels had not changed whereas the numbers of working mothers had increased dramatically.
She said: "For many families the only parent or both parents will be working.
"Time constraints may limit parents' capacity to provide their children with healthy foods and opportunities for physical activity.
"Our results do not imply that mothers should not work.
"Rather they highlight the need for policies and programmes to help support parents."
The same children took part in an earlier study by the Institute of Child Health (ICH) which found that those with working mothers were more likely to be obese or overweight by the age of three.
In the latest study, many of the five-year-olds were engaging in health behaviours likely to promote excess weight gain: 37% were mainly eating crisps and sweets between meals, 41% were consuming sweetened drinks and 61% used the television or a computer at least two hours daily.
Glenys Jones, nutritionist with the Medical Research Council Human Nutrition Research, said the study was interesting because of limited research so far on the impact of maternal employment on child health choices.
"More work is needed to take into account factors such as how related health behaviours are affected and if the age of the child alters the relationships observed."
Sally Russell, a spokesman for Netmums, said: "The stress and guilt associated with being a working mum is something we are all too well aware of. This report adds to that guilt.
"With many more mums having no choice but to work these days and with government policy actively encouraging it, it is difficult to know how mums can do better. "
A Department of Health spokesman said: "Our Change4Life movement is already helping over 370,000 families eat well, move more and live longer by helping them to understand the harm that fat and added sugar can cause to children's health, and offering them simple yet effective ways to make changes to their diet and increase their activity levels."
BBC website readers have been sending in their comments on this story. Here is a selection of their thoughts and experiences.
I was a lone parent working mum. My son is now 25 and for about half his time at school I worked full time. He always walked to school and ate healthily. He is very fit and a perfect weight for his height. I guess he is pretty typical. Eva McDiarmid, Glasgow, UK
Damned if we do, damned if we don't. Never mind the fact that most of us don't have the luxury of choice in the matter. Thanks for reporting this so widely and making my commute to work just a little bit more rubbish today, BBC. Debbie Newton, Leeds, UK
I'm cross on so many levels, but mainly a personal one! I work, my husband doesn't, he is our daughter's main carer. He walks her to school, he looks after her after school stuff and cooks her meals every day. She has restricted TV time and is not allowed sweets. Why do people insist on saying 'mother' when they often mean 'parent'. It's wrong on other levels too of course, but for me it's the stupidity of assuming a mum should stay at home and a dad should work - are we still in the 50s? Naomi, Sussex, UK
As a lone mum to one daughter, I work full time because I cannot manage financially any other way. I feel like I'm damned if I do and I'm damned if I don't. I get encouraged to work over 30 hours a week and get a financial incentive for doing this through tax credits, but I feel like I am also heavily criticised for not being a 'proper' mum by not spending enough time with my daughter. I leave the house at 8am every day, get home at 5.30pm every day, my daughter goes to bed at 7pm. I'd love to know where I'm supposed to shoehorn in some quality time with my girl! Jane Crabtree, Middlesbrough, UK
This does make me feel even more guilty for working. Being in full-time work and handing over my three year old to childcare is bad enough, and then having to spend a lot of time during the evenings and weekends doing 'house stuff' really doesn't leave me much time to spend with him, doing the things we want to do. I almost wish we could go back to the days when the mother was expected to stay at home, and the father provide. Sadly, this isn't financially possible in my case. Hannah Steward, Oldbury, UK
Well this story is of no surprise. But why should it be mothers who stay at home? Surely in these days of equality fathers should be discussed as well. My wife and I decided one of us would be at home to bring up the children ourselves. We based our decision about who would stay home on earning power. I hear many parents say they can't afford to not work yet they will lavish money on unnecessary extras. It's often about priority not ability. Too many children these days are treated like 'hobby children'. N Bair, Glossop, UK
I can't win. I don't want to work, I want to look after my family and ensure my kids have a good life. But unlike the many teen parents, I was pregnant at 16 and I married the father of my kids. We purchased a house when I was 18 and we work hard to pay our mortgage. I see this as what all parents should do to instil pride in themselves and their children. I don't live off other people's tax, I pay for the lazy people who live off the state. If a mother or father stays at home because their income allows them to then I feel this is the dream for all parents and this is very lucky. Catrina Stephens, Trowbridge, UK
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