"We received a deposit for the amount of USD 1 billion (893 million euros) from the Kingdom of Saudi Arabia in two instalments, USD 500 million this month and USD 500 million last month," Abdul Rahman Dirar told a press conference.
Dirar did not elaborate.
In April, the finance ministry announced that Qatar would make a USD 1 billion deposit to its central bank to boost its foreign exchange reserves, although no further statements were made about that.
Khartoum has said Saudi Arabia planned to invest in its agricultural sector, but Khartoum has denied that it was linked to its participation in the campaign in Yemen.
South Sudan split from Sudan in 2011, taking with it the majority of the formerly united country's oil production, which accounted for billions of dollars in export earnings and hitting Khartoum's finances badly.
The country has also been under a US trade embargo since 1997 imposed over rights abuses and support for radical Islamist groups in the early 1990s.