Brigadier Hangwani Mulaudzi, spokesperson for the elite crime-busting unit, said officials of the court insisted it was standard procedure to chain Zuma.
His ankle cuffing sparked controversy on social media, with many saying it was unwarranted because it did not appear that he would suddenly flee from the dock.
Facing a charge of conspiracy after allegedly offering then deputy finance minister Mcebisi Jonas a R600million bribe at the Guptas' Saxonwold home in 2015, Zuma had handed himself over to the Hawks.
Magistrate Jeremy Jansen van Vuuren granted Zuma bail of R100000.
Many on social media questioned if Zuma would suddenly make a run for it after handing himself over.
IFP MP Mkhuleko Hlengwa posted on Twitter: “When the justice system indulges in theatrics it compromises its own legitimacy, integrity and credibility. This leg-chaining is one such theatric. (Zuma) handed himself over and there was certainly no need for (that). Let him be prosecuted fairly.”
Mulaudzi said Hawks officers brought Zuma with no cuffs to the court from the Joburg Central police station.
“It’s not us at all. We’re not responsible for the shackling,” said Mulaudzi.
“People must understand that there are court orders and set operating standards at each and every court.
“If people saw it on TV, they would have seen that when he came to court he was not in shackles.
“Unfortunately, when he got to the court there was an instruction that he be shackled. We also, together with his lawyer, tried to negotiate that he must not be shackled. We did not win that fight. Sadly, we were unable to convince the court not to have him in shackles.”
Mulaudzi said questions about this requirement of the court should be directed to the Department of Justice.
“The guy was co-operating”, Mulaudzi added. “When we brought him to court, we did not see him as a flight risk. But unfortunately that instruction was given.”
But Zuma is not the first high-profile accused to appear at the Joburg Specialised Commercial Crimes Court shackled around the ankles.
The ANC’s Andile Lungisa arrived in the dock shackled in 2013 for alleged fraud and money-laundering. He was acquitted.
Dan Bovu, an ANC heavyweight in Joburg, was also shackled when he appeared earlier this year. He was also acquitted.
An official at the court said all accused appearing for the first time or arriving from the central prison are required to be shackled.