The order makes vaccinations more accessible and allows pharmacists to administer vaccines to children.
Almost 20,000 cases of flu have been reported in New York state so far this season – more than four times the number of cases last winter.
The flu outbreak has reached epidemic proportions across the US.
Last week 7.3% of US deaths were caused by pneumonia and the flu, just above epidemic threshold, said the US Centers for Disease Control and Prevention (CDC).
Flu activity was widespread in 47 states, up from 41 the week before.
Experts recommend flu vaccines, which have been found to be 62% effective.
The 2012-13 flu season is said to have started earlier than usual, with many cases of the H3N2 strain, which can be severe.
Some analysts say the latest numbers suggest the worst of the season may have passed.
The only states without widespread flu were California, Hawaii and Mississippi.
Flu symptoms can include fever, cough, runny nose, body ache and fatigue.
Severe cases could see vomiting and diarrhoea or develop into pneumonia. Many cases are much milder.
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