Nurses have seen their average basic pay increase by just 0.7% while NHS managers have seen their pay rocket by 2%.
Nurses, midwives and health visitors saw their average basic pay rise to £30,481 in the 12 months to September.
This is the equivalent of a £216 cash rise but smaller than the £638 cash rise, or 2.2% rise between 2010 and 2011.
Midwives saw average pay dip by £12 to £32,326.
The largest percentage increase between 2011 and 2012 was among school nurses, who saw a 1.2% or £391 rise in basic pay to £32,232.
Senior managers working in the NHS enjoyed the largest increase in pay of any hospital workers with a rise of 2%, or £1,459 to £74,654.
Overall basic pay increased, as an average, for all full time equivalent NHS staff by 1.3 per cent in the 12 months to September 2012 to £29,316, a rise of £379 compared to the same period in 2011.
Although the average basic pay increased, the rise was smaller than that seen between 2010 and 2011 when pay jumped 2.6 per cent or an average of £722.
The increases in pay shows the effect of incremental pay progression in the NHS which has seen pay bills go up despite two years of a Government pay freeze.
Workers on less than £21,000 have also received £250 increases in each of the past two years further driving up costs for NHS providers.
For hospital doctors, including consultants and registrars, average basic pay increased by 1.4 per cent to £58,456.
Scientific, therapeutic and technical staff saw basic pay rise 0.4 per cent to £34,354 while clinical support staff saw their basic pay increase 1.6 per cent to £18,351.
Average pay for ambulance staff saw a 0.6 per cent rise to £26,446.
The pay estimates have been made using the Electronic Staff Record system and for the first time uses 12 months of data to improve accuracy.
Tim Straughan, chief executive of the NHS Information Centre said: “As the NHS employs more than a million people in England, its composition is obviously of great interest to the health service and public alike.
“Today’s figures are intended to provide new insight into the average earnings of this workforce, which of course contains a complex mix of differing grades of experience and working patterns,” he added.
“Although they are experimental, the figures do point to a small increase in average basic pay for most staff groups between 2011 and 2012.”