Justine Greening, the development secretary, told parliament she was scrapping the five-year programme, which has been helping to build roads, raise trade standards, and eliminate agricultural diseases.
She said millions had already been spent on various projects run by TradeMark Southern Africa, but £46m will now be clawed back by the government following investigations by auditors and the Independent Commission for Aid Impact.
“While we have found no evidence of fraud, these investigations have revealed a number of serious concerns including weakness in delivery, management, oversight and financial monitoring,” she said.
She said weak governance also resulted in £80,000 of payments through the Zimbabwe ministry of agriculture for a fruit fly eradication programme in contravention of UK government policy.
“I am fully prepared to stop funding to programmes that do not offer value for money or that fail to achieve their objectives and I have given notice to commence shutting down TradeMark Southern Africa with immediate effect,” she said.
Greening will also begin an investigation into her own department to “strengthen oversight and financial control” in Southern Africa.
Since 2010 David Cameron has repeatedly reaffirmed his commitment to spending 0.7% of the UK’s income on foreign aid, but he has so far failed to enact a coalition pledge to enshrine that promise in law.
At the same time, the budget for helping the world’s poorer countries has come under sustained criticism from Tory rightwingers, many of whom argue that Britain can no longer afford to send billions abroad at a time of austerity.
Cameron has also faced criticism from charities over the prospect of “stealth” cuts to aid after he signalled he was prepared to take more funding from the aid budget for peacekeeping missions and security, rather than the Ministry of Defence.
Since she became development secretary in 2012, Greening has emphasised her role in getting value for money out of aid spending.
Earlier this year, she said the UK’s aid programme to South Africa, £19m a year, would end in 2015. That decision, which the government said had followed talks with Pretoria, provoked a diplomatic row with the South African government.