The Department of Health monitors illnesses in 120 state and private boarding schools to check the spread of infectious diseases, including mumps, measles and influenza.
The Medical Officers of Schools Association will now also be checking for new strains of flu.
Dr Neil Arnott, honorary secretary of the association, said: "Boarding schools have young people aged 13 to 18 in a closed community, which is what flu germs love.
"The reporting system has been going for quite some time and is quite useful as an early indication of what might be lurking.
"A number of boarding schools had pupils returning this week from all around the world, where different flu viruses may be circulating. That is one thing they have to be aware of."
If the virus does attack, it can spread rapidly in schools. In previous pandemics, nine out of 10 boarders became ill. The closure of any school will be decided locally if there are fears of spreadingthe disease.
The Government's influenza pandemic contingency plan says that unless children or young adults turn out to be one of the groups most at risk, closing schools and other educational facilities would do little to reduce the number of cases overall.
Local authorities have powers to request that a person refrain from working to prevent the spread of infection, and to require a child who has been exposed to infection not to attend school.
Bird flu can only be caught from infected birds, but experts fear it may mutate to be able to pass between humans. So far, about half of the 122 people who have caught the bird flu virus H5N1 have died.