The South African government have accused their British counterparts of failing to go through the proper channels before announcing an end to the country's annual £19 million payment in Official Development Aid.
The Department of International Relations and Co-operation said it had noted the UK announcement "with regret", adding that the "major decision" had "far reaching implications on the projects that are current running" in South Africa.
A statement from the department added:
Ordinarily, the UK government should have informed the government of South Africa through official diplomatic channels of their intentions and allowed for proper consultations to take place, and the modalities of the announcement agreed on.
We have a SA/UK Bilateral Forum which is scheduled for some time this year and the review of the SA/UK strategy which includes the (Official Development Aid) would take place there and decisions about how to move forward were expected to be discussed in that forum.
The department said there was "no doubt" that the UK's announcement "will affect how our bilateral relations going forward will be conducted".
But it said it would use the forthcoming forum to "clear up this matter among others".
The UK's direct aid to South Africa will end in 2015, International Development Secretary Justine Greening will announce.
The Government's aid programme to South Africa is currently worth £19 million a year, down from its peak of more than £40 million in 2003, and has focused on reducing the mortality rate among women giving birth, as well as supporting businesses.
Mr Greening will tell a conference of African ministers and business leaders in London tomorrow that the relationship will change to one of "mutual co-operation and trade".