The allowances for African troops fighting al-Qaeda-linked militants in Somalia have not been paid for at least six months.
The 22,000-strong African Union force (Amisom) fighting the Islamist militant group Al-Shabaab is funded by the EU.
An European Union source told the BBC that last six-month payment was being withheld over "accounting issues".
The head of Amisom said that the correct papers to account for the last tranche had now been submitted.
"These papers are on their way; the money is also on its way," Francisco Madeira said.
The EU provides $1,028 for each Amisom soldier each month; their respective governments then deduct around $200 for administrative costs meaning the soldiers are supposed to take home about $800.
This deployment allowance is much more than the meagre salaries the soldiers receive from their governments.
The funds are only released to Amisom by the EU once the accounts from the previous payment are signed off.
There have been delays over the last two tranches - and last year's June-November payment has only just arrived.
So soldiers are now receiving money owed to them last year but have not received any of it owed to them this year.
Ugandan military chief General Katumba Wamala said he unable to describe the extent of his frustration over the late payments.
Gen Wamala also said that Uganda would pull its soldiers out of Somalia by December 2017, because of frustrations with the Somali army and military advisers from the US, UK and Turkey.
Uganda joined Amisom in 2007 and is the force's biggest contributor, with more than 6,000 troops.
Burundian military officials also said their troops had not been paid.
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