Women who became pregnant before September 2010 are not counted in official flu jab uptake figures.
But most expectant mothers in England fell into this category when GPs began vaccinating at-risk groups.
The DoH said this cut-off was applied to avoid double-counting those offered the Pandemrix pandemic flu vaccine before this date.
But one practice manager, who asked not to be named, told GP: ‘The majority of pregnant women didn’t want Pandemrix even during the last seasonal flu campaign, never mind during last summer.
‘The seasonal flu data on pregnant women is rubbish. Unless they are adding data from elsewhere I fail to see how it can be correct.’
A DoH spokeswoman said the cut-off date was introduced to ‘avoid double counting and a cross-over with the new flu season’s data’. She said GP pay would be unaffected.
The seasonal flu jab is being offered to pregnant women for the first time to protect against swine flu complications.
Uptake data suggest 34% of pregnant women, excluding those pregnant before September 2010, had the jab this winter, including 53% in at-risk groups.
NHS Employers and the GPC have agreed eligible patients who received Pandemrix instead of the seasonal jab will count towards QOF this year.
Officials said last week there were signs the flu outbreak was declining. Deaths from flu rose to 254 by 20 January.