The admission comes just weeks after the government was criticised for not running flu awareness campaigns for the past two winters.
Last year, GPs warned that health secretary Andrew Lansley's decision not to promote the flu vaccine by a national campaign may hit uptake rates.
In response to poor uptake, England CMO Dame Sally Davies has written to GPs and the NHS saying they should aim to vaccinate 75% of people aged 65 and over this coming winter.
The letter also advises a target of 70% for people under 65 at-risk from flu, which includes pregnant women. This is a rise from 60% last year and is a step towards the DH's target of 75% by 2013/14.
However, children will not be eligible for the jab this winter, despite recent research from York University suggesting that immunising healthy children would prevent 80% of flu infections and free up 790,000 GP appointments a year.
GPs will face renewed scrutiny over their vaccination plans.
In the letter, the CMO thanked the NHS for its efforts last season but said it was 'disappointing' the NHS failed to reach the 60% jab uptake target set last year.
Dame Sally said: 'We recognise that the second challenge above may be difficult, and will require fresh thinking and new approaches to deliver these levels. However, with your commitment and support we believe it is right to strive for this level of protection for these particularly vulnerable groups.
She added: 'There is no guarantee that next winter’s flu season will be as mild as the last.'
Practices have been set a deadline of 15 June to present robust vaccination plans to their PCTs as part of the DH's bid to improve uptake.
This includes ensuring the practice will keep updated registers of all eligible patients including pregnant women; has ordered sufficient vaccine stocks; and will call and recall all patients who do not respond to invitation letters.
GPs may need to organise patient group directions to allow midwives at antenatal clinics to vaccinate pregnant women if they do not present to their surgery, the CMO said.
PCTs have been urged to vet GPs and other providers on how well their flu vaccination plans worked last winter so they can scrutinise plans for this coming season.
The NHS faces an uphill struggle to hit the CMO's targets.
In 2011/12, just 51.6% of people at-risk of flu aged under 65 were vaccinated against flu. Uptake among pregnant women was just 27.4%.
Uptake reached 74% among over 65s, though this still falls short of the WHO target of 75% for all at-risk groups, which the DH is aiming to achieve by 2013/14.
Although vaccine uptake among healthcare staff rose to 45% in 2011/12, uptake is 'still too low' and must improve, the CMO said.
The CMO revealed that two different strains are expected to be among those circulating predominantly this coming winter.
As such, the WHO has announced that the seasonal trivalent vaccine should protect against the same H1N1 strain as in 2011/12 but against different H3N2 and influenza B strains.
The DH confirmed it will hold a 'small central strategic reserve' of flu vaccine as an insurance against shortages in a more severe season.
The DH will update the Green Book on Immunisation Against Infectious Diseases soon, it said.
The list of eligible patients who should be offered the flu vaccine has not changed since last year.
In April, a report led by former CMO Sir Liam Donaldson found the DH's 'laissez-faire' attitude to swine flu contirbuted to a 30% rise in deaths in the season after the pandemic year.
Cancellation of the annual flu campaign and a failure to warn that the pandemic virus would circulate and affect younger people led to a ‘worrying’ fall in awareness, the review said.