It has reinforced concerns that using the devices could become a "gateway" to smoking cigarettes.
The study found 6% of 10 to 11-year-olds in Wales said they had used e-cigarettes, compared to 2% who had smoked tobacco.
Children who tried e-cigarettes were seven times more likely to say they might start smoking within two years.
They were also more likely to use e-cigarettes if their parents were smokers.
The vast majority of children who had tried e-cigarettes had never tried tobacco, according to the latest Childhood Exposure to Tobacco Smoke (CHETS) study.
But the study found evidence to suggest that e-cigarette use may lead children to smoke tobacco.
Source: CHETS study
Health Minister Mark Drakeford said:  "These latest findings shine further light on the potential impact of e-cigarettes on our children and young people.
"I am concerned the use of e-cigarettes may act as a gateway to and re-normalise smoking, especially for a generation who have grown up in a largely smoke-free society."
The study also found that fewer children were being exposed to second-hand smoke in cars and their homes.
Source: CHETS study
Three times as many children have tried e-cigarettes as have smoked tobacco, according to official figures.