South Africa’s National Treasury threatened to terminate all funding for covert operations last year, after the country’s spy agency refused to account for tens of millions of dollars in expenses, saying the money had been put to “secret use”. An investigation by two leading South African news outlets, the Afrikaans-language weekly newspaper Rapport and the English-language online news portal News24, has revealed the existence of a major bureaucratic spat between the National Treasury and the State Security Agency (SSA), the country’s primary civilian intelligence organization.

The investigation cited “seven independent sources” with direct involvement and knowledge of the National Treasury and the South African intelligence services. According to the report, National Treasury officials contacted the SSA last year, demanding to know how it used 1.5 billion rand (approximately US $114 million) that it took from government coffers between 2012 and 2016. But the spy agency refused to provide a detailed answer, and said instead that most of the money had been used to fund unspecified “secret operations”, and that its use was therefore classified.

However, the SSA did not realize that National Treasury officials have the same level of security clearance as senior SSA officials, said sources. Consequently, a Treasury probe was launched by Treasury investigators with access to SSA’s activities. The probe uncovered several instances of irregular expenditures and serious mismanagement, said the report. There were repeated instances when funds assigned to non-covert operations were “inexplicably moved to the covert fund” and SSA officials were unable to explain why. There were also numerous cases of abuse of procurement procedures. One source told the News24/Rapport team that “Treasury officials kept asking [SSA officials] how they tender for goods and services, and they kept saying that they can’t tell us, because it is classified information”. At that point, the National Treasury threatened to terminate all funding for intelligence operations unless answers were provided by the SSA leadership. After a series of frantic and tense negotiations, the SSA agreed to change its procurement practices and “at least submit [to National Treasury] a list of suppliers so that there could be a degree of oversight”.

The SSA’s reputation has not emerged unscathed from the broader crisis that has been plaguing South African politics in recent years. In 2014, the Johannesburg-based newspaper City Press alleged that the SSA maintained a secret unit used to target domestic political opponents of South African President Jacob Zuma. The paper also said that senior SSA official Thulani Dhlomo, a close ally of President Zuma, had been placed at the head of the secret unit in 2012. Another leading Johannesburg-based newspaper, The Mail & Guardian, repeated these claims earlier this month.