The MHRA asked the company to undertake a 'precautionary recall' of two batches of Agrippal vaccine, but stressed there was no evidence of safety concerns.
The recall came after visible 'protein aggregates' were detected in one batch for the Italian market during a routine inspection by Novartis. The company said it had availability to replace all recalled doses.
An MHRA statement said: 'At the request of MHRA, Novartis Vaccines and Diagnostics is executing a precautionary recall of the above batches.
'Based on the information available, there is no evidence of any new safety concerns or of any impact on efficacy. No adverse reactions which may be associated with this issue have been reported to Novartis in connection with these batches.'
The MHRA said there was no need to revaccinate people who have received flu vaccine from these batches. Remaining stocks should be quarantined and returned to the original supplier, it said.
A spokeswoman for Novartis said: 'During a routine pre-release quality analysis of one batch of Agrippal for the Italian market, Novartis identified visible protein aggregates in one batch of vaccines which was not released to the market.
'The protein aggregates are not uncommon in vaccines and have no impact on their safety or efficacy. Individuals already vaccinated with Agrippal in the UK should not be concerned and there is no need for revaccination.'
The affected batch numbers are 126201A and 126102. Both contain pack sizes of 10 pre-filled syringes with the expiry date of 31 May 2013, and were first distributed on 9 and 17 October 2012 respectively.
The recall comes after manufacturer Crucell voluntarily halted deliveries of two batches of flu vaccine to the UK in October on patient safety grounds.