Pharmaceutical company Crucell has halted all supplies of its seasonal influenza vaccines as it investigates two batches on patient safety grounds.
The DH has advised GPs to contact alternative suppliers if they have supply problems.
Crucell supplies 10% of flu jabs in the UK with its Viroflu and Inflexal vaccines. In a statement, the company said: 'Crucell is voluntarily holding all deliveries of our seasonal flu vaccine while we complete an investigation pertaining two batches.
'As always, our top priority is patient safety and therefore we will wait until we have final results on the product quality of these two batches before releasing any of the vaccines in the 2012/2013 flu campaign.'
The company will issue an update on the investigation on 15 October 2012.
A DH spokeswoman said: 'We are aware of some unexpected delays to one supplier's deliveries of the flu vaccine and advise GP practices to contact alternative suppliers if they are having problems.'
No shortages of flu vaccines have been reported so far.
In 2010/11, the DH released doses of the 2009 pandemic flu vaccine in response to localised shortages of the seasonal flu jab across England. The shortages led to a DH consultation on whether GPs should be stripped of the role of ordering flu vaccines in future.