Eyewitness News reports the defence department hired the Bombardier Aerospace plane through a state-managed contract with service provider ExecuJet.
The Bombardier Aerospace, with registration ZS-OAK, left Waterkloof Air Force Base on Friday night under the call sign "South Africa 2", which is reserved for the deputy president.
Ramaphosa was then photographed arriving in Tokyo in the aircraft on Saturday night.
Ramaphosa and the delegation, which included Cabinet ministers, were in the country to increase collaboration and partnerships in the fields of science and technology in order to boost economic growth and create jobs, his office said.
According to EWN, the plane is registered to Westdawn Investments, which is owned by the Gupta family. President Jacob Zuma's son Duduzane is a director at the company. Defence department spokesperson Siphiwe Dlamini told the broadcaster such leasing was done via a central contract managed by government through the National Treasury.
"The South African Air Force is not privy to the processes of acquiring such a service. However, it determines the technical specification of the aircraft and safety requirements,” he said.
A Gupta family spokesperson said Westdawn Investments has an agreement with ExecuJet to charter the aircraft on a commercial basis. They had no knowledge of dealings with third party clients.
In April 2013, a plane carrying about 200 guests who were travelling to the wedding of a Gupta family member at Sun City landed at Waterkloof Air Force Base, a national key point, causing controversy and resulting in a number of suspensions.
Ramaphosa and the government delegation are expected to arrive back in South Africa on Wednesday.
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