Both the Home Affairs department and visa application service company VFS have denied any links to President Jacob Zuma's son Duduzane and Rajesh Gupta following claims made by the Democratic Alliance last week.

The department's director general Mkuseli Apleni told reporters in Boksburg on Monday that he had personally overseen the process, as he had been with the department since 2010.

He said the contract he had signed on behalf of the department with Visa Facilitation Service (VFS) Global had no links to Zuma or Gupta.

"I know who are the shareholders there... The South African part of it has nothing to do with Zuma and Gupta as far as I know."

The department held a media briefing in the east of Johannesburg on Monday afternoon to respond to accusations made by Democratic Alliance MP Haniff Hoosen on Friday.

During a Home Affairs budget debate in Parliament, Hoosen said the department had signed a contract with VFS in 2011. He claimed that VFS was linked to a company called Islandsite Investment whose directorship included Duduzane Zuma and Rajesh Gupta.

"According to their website, there are VFS offices in 123 countries in the world. On the face of it, it looks very legitimate," the Daily Maverick quoted him as saying.

"But when a traveller makes a payment to VFS, a receipt is issued, and that receipt is in the name of a company with two very famous people. Duduzane Zuma and Rajesh Gupta."

Apleni denied this.

"I have not signed a contract at the home affairs department since 2010 with anything linked to [Islandsite Investment]," Apleni said.

He said he had no way of knowing who the company's directors and shareholders in other countries were, however.

"The department has appealed to VFS Global to continue being transparent and they have agreed to share details of their company directorships," Apleni said.

"We wish to discourage baseless accusations that impact negatively in the department's integrity given the critical role of the department.

"The department conducted itself in the best interests of the country and the clients and will continue to do so."

VFS Global's Chief Operating Officer in Africa Jiten Vyes also denied any link to Gupta or Zuma, describing the claims as "unfounded and untrue".

"VFS categorically denies any links whatsoever to this particular family as well as any party involved."

Vyes said that Islandsite Investment 309 was a shell company which the company had used before officially registering as VFS Tasheel RSA (Pty) Ltd.

VFS Tasheel RSA (Pty) Ltd also facilitated visa applications from South Africa to Saudi Arabia.

Vyes said Islandsite Investment had a number of companies listed under it with different numbers. The Islandsite Investment company linked to VFS was company no.309, he said.

The company cited by the DA as having Zuma and Gupta links was Islandsite Investment no.255. The two were not linked in any way, he said.

Earlier, Apleni had said that the Islandsite receipt Hoosen had used as an example in Parliament, had been issued by Saudi Arabia and not South Africa.

"This receipt was for a person travelling to Saudi Arabia, and therefore had nothing to do with us. We do not and cannot, offer such a receipt," he said.