The statistic is part of a review of progress made on the nation's health that she acknowledged was "disappointing".
Current guidelines recommend young people should exercise for at least one hour a day during a typical week.
But only four out of 10 boys and two out of 10 girls are doing enough exercise, Hall found, with activity declining further below recommended levels the older children get.
Vikki Butler, policy officer at Barnardo's in Swansea, said traditional sporting activities were focused on boys. The type of sport girls wanted to play, such as dance and gymnastics, were not seen as sport, leaving girls to access these activities informally.
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