The African Union Mission in Somalia (Amisom) was responsible for killing or maiming 42 children last year, the United Nations secretary-general said in a report issued on Friday.
Air strikes by the Kenyan Defence Forces killed or injured another 11 children in Somalia, added the report on "Children and Armed Conflict".
One additional child casualty was linked to a US air attack.
"Child casualties attributed to Amisom primarily occurred in operations against Al-Shabaab or in indiscriminate fire responding to attacks," the report presented to the Security Council by UN chief Antonio Guterres said.
The secretary-general noted that Michael Keating, his special representative for Somalia, has "raised concerns with Amisom about grave violations".
The report further blamed Somali National Army troops for the killing or maiming of 146 children last year.The number of child casualties said to be inflicted by the allied forces of Amisom, KDF, Somali army and the US thus totalled 200 in 2016.
Al-Shabaab was held responsible for the deaths or wounding of 290 children.
Clan militias and groups referred to in the report as "unknown armed elements" accounted for a combined total of 625 child casualties.
The number of children recruited as fighters in Somalia doubled last year to more than 1900, according to the report.
Al-Shabaab was primarily responsible for that upsurge due to a two-fold increase in its recruitment of children, the UN observed.
"The use of 17 children by Amisom was documented," the report added.
In its section on South Sudan, the report found government forces to be responsible for most of the 179 killings or maimings of children known to have been carried out in the country last year.
South Sudan's army was also blamed for a large majority of 142 reported cases of sexual violence against girls.
"The level of violations against children is completely unacceptable and merely indicative of the scale of suffering of children, as access constraints limit our ability to have the full picture," Virginia Gamba, the secretary-general's special representative for children and armed conflict, said.
"Such abuses have a dramatic impact, not only on the lives of children, but also on the social fabric of society in affected countries and on global peace and security," she added.