The guidelines from the Department of Health are in response to controversy about the risks of the potentially deadly blood clotting condition deep vein thombosis (DVT).
The advice, issued on Friday, covers all groups suspected of having an increased risk of DVT, which affects an estimated one in 2,000 people each year.
Mothers who have recently given birth, women taking hormone replacement therapy, and anyone who has recently had surgery or a stroke should also check before flying, or indeed any travelling which involves long periods seated, it recommends.
However, although these groups are thought to be at slightly higher risk, the overall risk is believed to be small.
Sitting still
Dr Pat Troop, the government's Deputy Chief Medical Officer, said that it was the "most up-to-date" information about the potential risks.
She said: "Blood clots can occur when people remain immobile and seated for long periods of time, and therefore could occur in a range of travel situations."
The new advice has been sent to airlines and will also be made available to the public through NHS Direct - the telephone information service.
Exercise advice
The guidance also encourages passengers to carry out "in-seat exercises" while flying, to increase blood flow to the lower legs, where clots are most likely to form.
Existing government guidelines already recommend that people with heart disease, cancer or who have recently had major surgery should seek medical advice before flying.
Fatal
Clots develop in blood vessels deep in the legs when circulation slows, usually because people stay still for long periods.
The clots can be fatal if they break off and are carried to the lungs, blocking the flow of blood - a condition called pulmonary embolism.
Publicity surrounding the condition was heightened by a number of high-profile cases.
Emma Christoffersen, 28, from Wales, died in October 2000, when she collapsed after a 20-hour flight from Australia.
Dr Patrick Kesteven, an expert in DVT from the Freeman Hospital in Newcastle, told the BBC that the government action was prompted by research in Holland, which suggested a stronger link between DVT, long haul flights and people in these high-risk groups.
Dr Kesteven said women taking the contraceptive pill were three times more likely to be at risk.
He added: "There are various things you can do depending on the level of risk and I suspect the medical advice will be to work out what the risk is for that individual.
"I suspect some blood conditions can be disposed to thrombosis and a strong family history of thrombosis is a very high risk.
Action
"The other factors are age, recent surgery, recent immobility, for example having a leg in plaster."
He suggested various action including exercise, wearing support stockings and, in extreme cases, taking medication when flying.
Recent research had been inconclusive about the dangers of long haul travel.
But a comprehensive study is being proposed by the airlines and the World Health Organisation - and the Department of Health has backed calls for further research.
British Airways said it welcomed the new Government guidelines and stressed that it had, for nearly a decade, provided its passengers with advice about well-being in the air.
Simon Evans, from the Air Transport Users Council, said he was "delighted" that the government was taking the issue seriously.