The Guptas were the subject of a SARS investigation in November 2013, which they were tipped off about, the e-mails show.
It is not known whether the investigation was completed, but the family's Oakbay company received a controversial R70-million tax refund last month following SARS commissioner Tom Monyane's intervention, City Press newspaper reported.
Werksmans Attorneys tax lawyer, Ryan Killoran, said Atul Gupta could only have received his non-interest bearing loan tax-free if Sahara had paid dividends' taxes at the official interest rate on the loan.
He said tax authorities would typically make lifestyle audits on wealthy families such as the Guptas so as to determine whether their taxable income would support their assets and lifestyle.
"The issue of delayed VAT refunds generally is so serious that the tax ombudsman is investigating. To receive the R70-million refund in such a relatively short time means that they must be a taxpayer in high standing with SARS.
"They must have a perfect tax compliance record and senior connections to pressure the audit team to finalise the audit."
Killoran said based on what had been publicly reported about the refund it appeared Monyane may be favouring some taxpayers over others.
SARS spokesman Sandile Memela refused to answer questions on the Guptas' tax affairs.
These included whether the audit of the family and its companies had been completed, if Atul Gupta had paid taxes in respect of his loan, if the Guptas would be taxed for gifts of accommodation and air tickets to state officials as non-business expenses, or whether SARS officials, who alerted them to the investigation, had been disciplined.
Into Guptas' tax maze: Alleged tax dodge involves shifting expenses between companies
Evidence in the leaked Gupta e-mails points to a complex multibillion-rand tax-avoidance scheme with family patriarch Atul Gupta at its centre.
Several tax experts told The Times the picture painted by the transactions captured in the e-mail leak point to a practice known as "staggering" or revolving loans. The Guptas appear to have used personal and inter-company loans to and from their companies, many of which are offshore.
The practice involves shifting finances and expenses from one company to another prior to the end of the financial year. The loans are then reflected as assets and not as income, which is taxable.
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The loans enable a company to reflect a particular financial status at year-end and move money offshore to where entities hold accounts.
The Guptas failed to respond to questions on the allegations this week and the SA Revenue Service (SARS) failed to answer questions in detail.
An e-mail sent from Gupta lieutenant Ashu Chawla to Atul Gupta on December 18 2012 contains a spreadsheet with detailed information on loans to and from the family's Sahara Computers totalling more than R1.6-billion.
Of this, Atul Gupta, a South African resident and director of Sahara Computers, received personal loans from the company totalling over R144-million.
The company's financial records show he had paid back only R13-million.
Company loans to shareholders are partially taxable when interest-free.
Cash flow analysis of Sahara accounts gives further insight into the Guptas' finances and the allegedly staggered loans.
The data show that between December 2012 and September 2015 Atul Gupta owed the company roughly R140-million and had not, it seems, paid any back.
Based on these figures, without incurring any penalties for the non-payment, Sahara Computers or Atul Gupta would owe SARS millions of rands in taxes for this loan. With penalties and interest for non-payment, his bill would be substantially higher on this loan alone.
Sahara Computers' bank statements from February 2013 to September 2015 show that multiple loans were granted between the family's other companies.
The Times is in possession of 356 days of bank statements, which account for nearly 40% of the company's transactions for that period.
The statements show that Sahara had a turnover of R1.8-billion for this period.
Sources with knowledge of SARS's auditing processes, but who are not authorised to speak to the media, say the fact that Atul Gupta continued to owe Sahara money made him an "ideal candidate" for a tax audit, particularly in respect of his loans.
The Guptas were the subject of a SARS investigation in November 2013, which they were tipped off about, the e-mails show.
It is not known whether the investigation was completed, but the family's Oakbay company received a controversial R70-million tax refund last month following SARS commissioner Tom Monyane's intervention, City Press newspaper reported.
Werksmans Attorneys tax lawyer, Ryan Killoran, said Atul Gupta could only have received his non-interest bearing loan tax-free if Sahara had paid dividends' taxes at the official interest rate on the loan.
He said tax authorities would typically make lifestyle audits on wealthy families such as the Guptas so as to determine whether their taxable income would support their assets and lifestyle.
"The issue of delayed VAT refunds generally is so serious that the tax ombudsman is investigating. To receive the R70-million refund in such a relatively short time means that they must be a taxpayer in high standing with SARS.
"They must have a perfect tax compliance record and senior connections to pressure the audit team to finalise the audit."
Killoran said based on what had been publicly reported about the refund it appeared Monyane may be favouring some taxpayers over others.
SARS spokesman Sandile Memela refused to answer questions on the Guptas' tax affairs.
These included whether the audit of the family and its companies had been completed, if Atul Gupta had paid taxes in respect of his loan, if the Guptas would be taxed for gifts of accommodation and air tickets to state officials as non-business expenses, or whether SARS officials, who alerted them to the investigation, had been disciplined.