The guidance document says that while most countries have signed a pledge to protect children, the agreement has not been transferred into law in many cases leading to the potential exploitation of children.
The children working in small-scale fisheries and on some aquaculture farms are left exposed to potential hazards, in some cases being forced to dive to great depths and in others working in the harsh environment of processing factories.
"All work that harms children's physical, mental, psychological, social and educational development, is unacceptable and violates international conventions" said Constance Thomas, Director of the ILO's International Programme on the Elimination of Child Labour.
"We need to ensure that agreements designed to protect children from child labour are implemented."
It is estimated that 130 million children are working in agriculture, livestock and fisheries around the world - 60 per cent of the total child labour force.
The FAO and the ILO have called for compliance with international rules to protect children working in the industry.
These include the ILO's Minimum Age Convention, and its Worst Forms of Child Labour and Work in Fishing Conventions, the UN Convention on the Rights of the Child and the FAO's Code of Conduct for Responsible.