The pertussis vaccination drive introduced by the DH in October 2012 has cut cases by 51%, including a 80% fall in infant cases, according to new figures from Public Health England (PHE).
Around 60% of pregnant women were vaccinated against whooping cough last year, and infant deaths fell to three in 2013, down from 14 in 2012.
But PHE warned that more mums-to-be must be vaccinated to avoid further deaths.
None of the mothers of the infants who died had been vaccinated during pregnancy, and the infants were too young to be vaccinated themselves.
Dr Mary Ramsay, PHE’s head of immunisation, said: 'The increase in vaccine uptake over the last six months is very encouraging, but we need to ensure we vaccinate as many pregnant women as possible to avoid further tragic deaths.
'We are also working with GPs, midwives and other health professionals to ensure they have the facts at hand to help women make the decision to vaccinate.'
Protect children with vaccination
She added that it was also important to vaccinate children against whooping cough, even in cases where the mother had been vaccinated during pregnancy, in order to ensure continued protection against the disease.
The number of laboratory-confirmed cases of whooping cough in England fell from 9,367 in 2012 to 4,623 in 2013.
Cases among infants under three months old, the group most at risk from whooping cough-related fatality and complications, fell by 79% from 407 cases in 2012 to just 85 cases in 2013.
The DH programme offered the pertussis vaccine to pregnant women at between 28 and 38 weeks gestation.
Vaccinating against whooping cough during pregnancy enables a high number of whooping cough antibodies to be transferred from the mother to the unborn child. This immunity then lasts until the baby is two months-old, when they are old enough to receive their first dose of the vaccine.