The number of reported incidents of the highly infectious disease had fallen dramatically, but this latest data suggests they are starting to climb.
Babies, for whom whooping cough can be fatal, are immunised at two, three and four months, and again before they start school.
Before the vaccine was introduced in the 1950s England saw tens of thousands of cases each year, but this then rapidly fell to about 2,000 cases annually after the immunisation programme began.
In 2003, there were just 386 cases in England but provisional figures suggest there were as many as 1,071 in 2007.
During this period, uptake of the jab remained steady over the last few years – around 93% or 94% coverage between 2003 and 2007.
Recent research from the University of Oxford said that while immunisation is effective, doctors needed to be aware that protection did not last indefinitely. A child with a persistent cough should be investigated for whooping cough, researchers warned, even if they had been fully immunised.
The Liberal Democrats, who obtained the figures, said they showed “public health schemes were failing to reach the people who need them most”.
But the Department of Health said cases of whooping cough had always fluctuated on an approximate four year cycle.