The Guptas' capture of South Africa could have been stopped 12 years ago if the National Prosecuting Authority (NPA) had prosecuted a R120-million exchange control-tax and customs fraud case linked to the family.

The NPA now says it can't explain how it happened because the file has been destroyed.

In 2001, Gupta-owned Sahara Computers and another company, Trump Technology - an alleged front for Sahara - were investigated by the then NPA, the Scorpions, for exchange control contraventions, VAT as well as customs fraud committed between 1999 to 2001.

There appears to have been two separate investigations that were ultimately joined into a single docket held by the Scorpions at the time.

The investigation was apparently concluded in 2003, but the NPA only declined to prosecute almost two years later in 2005.

Sars sources said the Scorpions started a criminal investigation after a witness came forward with information.

The Revenue Service was already busy with similar investigations and was asked to assist with the case given its complexity.

In 2002, a major breakthrough occurred when a whistleblower went to the South African Reserve Bank (SARB) and provided detailed information on how Sahara and Trump Technology were operating their alleged scam. The investigation was then handed to the Scorpions.

A joint investigation between SARS, SARB, NPA and the Scorpions resulted in a completed docket being handed to prosecutors in 2003.

The apparent scam involved under-declaring the value of imported electronic goods and parts, and then allegedly reflecting the items' sale at falsified value on invoices.

Sahara was then able to claim back higher amounts of VAT from SARS.

The NPA on Friday said it could not establish why they had declined to prosecute.

NPA spokeswoman Phindi Louw said the file was destroyed in line with regulations.