He was reacting to allegations in a report on state capture by the Public Affairs Research Institute that he appointed people with Gupta-Zuma-aligned interests to the boards of state-owned enterprises (SOEs) when public enterprises minister.
The report was filled with inaccuracies and "continues the trend of defamation", said Mayihlome Tshwete, Gigaba's spokesman.
The Public Affairs Research Institute last week released a report, Betrayal of the Promise: How the Nation is Being Stolen, compiled by several academics. The 72-page document details how the Gupta family, through various companies and friends, including President Jacob Zuma, profited from multimillion-rand contracts with state-owned companies.
The report describes the alleged corruption as "a silent coup".
It contains a timeline of changes to the boards of SOEs by Gigaba between 2010 and 2012, when he was public enterprises minister, and alleges that these appointments were intended to pack the boards with directors aligned to certain interests.
The report states that SOEs were targeted because their expenditure does not have to be tabled in parliament - whereas that of government departments does - and can, therefore, be hidden from public scrutiny.