Dr. Frank Atherton said the province's paper records are held by the district health authorities, but paper can go missing and there are sometimes duplicate reports.
"It doesn't give us an accurate picture of what proportion of children in Nova Scotia are currently vaccinated and we need to know that," said Atherton, who appeared before a legislature committee.
He said the province needs a central vaccine registry to target individuals and areas where there are low vaccination rates.
Nova Scotia is not alone in lacking a vaccine registry, Atherton said, but progress is being made elsewhere with systems in place in Quebec and Ontario.
Frances Martin, acting deputy health minister, told the committee that the province is working on a records registry in collaboration with the other Atlantic provinces.
The Health Department will forward a budget proposal for 2015-16 after it abandoned a project in 2009 that had begun five years earlier on an electronic records surveillance system in concert with Ottawa and the other provinces, she said.
Martin said the province felt the system, known as Panorama, was too costly and development was too slow.
"The provinces that continued working on Panorama are only now getting some components of the system up and running," said Martin.
Outside the committee, Martin said the province had earmarked about $11 million towards the development of that system, but only spent $400,000 on computer servers that were eventually used for other information technology systems.
Progressive Conservative Allan MacMaster said it's strange an electronic records system isn't already in place.
"For something that can make a difference in getting the population healthier and protecting against disease, it's puzzling why they are not advancing on it," said MacMaster.