The figures show that the proportion of unfilled nursing posts rose from 2.5% in 2008 to 3.1% in 2009.
And long-term vacancies - posts that have been unfilled for three months or more, a better indicator of which positions are hard to fill - rose from 0.5% to 0.7%.
The shortage of nurses is most acute in London, where the long-term vacancy rate climbed from 1.2% in 2008 to 1.6% this year.
NHS Information Centre chief executive Tim Straughan said that, although vacancies had risen, they remained lower than they were before 2006.
Meanwhile, the Information Centre has also released its annual survey of GP practice vacancies.
These show that long-term vacancy rates in English practices remain static at around 0.3%.
But in Wales they have quadrupled, from 0.2% to 0.9%.
And all vacancies have climbed from 0.6% to 2.2%.
Dr Peter Carter, RCN chief executive, said: 'Today's figures are worrying as they show that long-term nursing vacancies are rising for the first time in five years. While we are concerned about long-term vacancies, even unfilled short-term vacancies leave nurses under unsustainable pressure and, with higher workloads, too busy to provide the standard of care they would like.
'Rising vacancy rates are due to a combination of factors - more nurses are retiring and fewer are coming out of training. Add to this an increase in demand for nurses, coupled with recent changes in migration policies, restricting the recruitment of nurses from outside of the EU.
'Unfortunately, today's statistics are likely to mask the real picture of even higher vacancies. If a trust does not ‘actively' recruit for a post then it does not declare it vacant and it isn't counted in the vacancy data.
'We have been saying for some time there is a worrying mismatch between rising levels of healthcare demand and the numbers of nurses in post needed to give patients quality care.'