In a message to GPs, pharmacists and the wider NHS, Professor Dame Sally Davies said GPs can now prescribe antivirals at NHS expense for prevention and treatment of flu in people at risk of complications.
She said there was now a 'substantial likelihood' that people presenting with flu-like illness are infected with the virus - particularly school children.
It comes after the latest Health Protection Agency (HPA) figures showed visits to GP surgeries for flu-like illness among children aged 5-14 in England rose to 31.2 per 100,000 in the week to 9 December. Updated figures are due later today.
In her letter, Dame Sally said: 'The most recent surveillance data indicate that there is now a substantial likelihood that people, including children in schools, presenting with an influenza-like illness are infected with an influenza virus.
'GPs may now prescribe at NHS expense, antiviral medicines for the prophylaxis and treatment of influenza, in accordance with NICE guidance and Schedule 2 to the NHS (General Medical Services Contracts) (Prescription of drugs etc) Regulations 2004, commonly known as the Grey List or Selected List Scheme (SLS).'
The Grey List, which details the at-risk people eligible for free antivirals on the NHS, includes pregnant women, who were added in 2010.
Dame Sally reminded GPs they can also use clinical discretion to prescribe antivirals to patients outside this list whom may be at risk of complications from flu.
She added that the rise in flu activity highlighted the need for increased uptake of the flu vaccine, saying GPs had 'a particularly important role to play' and urged health professionals to get vaccinated.
She said University of Sheffield research had identified key measures undertaken in practices with high uptake rates.