Around 33,000 children are to be immunised against measles and polio in typhoon-hit Tacloban city.
The World Health Organization, which is supporting the government campaign, fears possible outbreaks of disease.
More than 5,000 people were killed when typhoon Haiyan battered the central Philippines.
Huge numbers - including many children - were left homeless, and many are surviving in cramped, unhygienic conditions in damaged buildings.
These "displacement centres", which include dilapidated schools or community buildings, were sturdier than people's homes, and more able to withstand the battering from the typhoon.
But, over-run by homeless people, they have created the perfect environment for the spread of disease.
Tarik Jasarevic, spokesperson for the World Health Organization's emergency relief team said: "Measles is a viral infection that spreads very very fast.
"When you have an over crowded setting, there is a risk of infection.
"It is enough to have one case and then we would probably see very fast transmission.
"Therefore, it is very important we prevent this before it happens."
The aim is to immunise all under-fives in Tacloban City. The children will be given polio drops and measles injections.
More than a hundred medics are expected to be involved in the first day of vaccinations. Around 40 will be from the Philippines, the rest will be from mostly European countries including Spain and Germany.
The children will also be checked for malnutrition and given vitamin A drops to help boost their immune systems.
The cold chain
Unicef is helping to provide the Philippines Government with the vaccines, but other supplies, like syringes, are also being flown in from around the world. These also include 16 solar-powered fridges from the UK.
A major challenge is keeping the vaccines cold. They need to stay below 8C during transportation to the immunisation site, and between 2-8C after medical team mix the vaccines with a diluting agent.
With no electricity and temperatures of around 30C and high humidity, that is a huge challenge.
Dr Heather Papowitz, senior health advisor from Unicef, said: "In this environment it's extremely difficult. Getting the vaccines from the plane to the cold room at the department of health is a real challenge in this circumstances.
"The vaccines need to go through quite a process to get here. They arrive by plane or boat, when they arrive they need to be picked up in cold boxes and taken by road to the cold room."
The cold room is a 9 sq m refrigerated room that is constantly kept between 2-8C. It is kept powered by a generator.
"Then we distribute them to the vaccination teams in these cool boxes," said Dr Papowitz.
"Then when people have to go out into the community, they take them in really small cool boxes to make sure they stay at the right low temperature the whole time."
The programme will start at the main displacement centres where the big centres in Tacloban city before medical staff head to more remote areas next week.