Choice says many juice boxes are laden with sugar and kilojoules, and parents should opt for fresh fruit in children's lunch boxes instead.
A Choice study found a quarter of fruit boxes contained 25 per cent or less juice and some were packed with more than six teaspoons of sugar.
Most were double the recommended 125ml serve of juice and lacked the fibre present in fresh fruit.
Choice says having water and a piece of fresh fruit is a more nutritious alternative to juice, but if parents want the convenience of fruit boxes they should choose brands with no added sugar and minimal kilojoules.
Industry group Fruit Juice Australia said Choice should concentrate on promoting moderation and a balanced diet rather than "demonising" sugar.
The group highlighted a 2007 Australian national children's nutrition and physical activity survey which found juice helped kids meet their daily fruit serve quota.
Juice was also a significant contributor of important nutrients, such as carbohydrates, folate and potassium, the survey found.