Captain Oleg Gladkiy, who is heading the Russian contingent in the South African joint naval exercise, said during a media briefing in the town of Richards Bay that no test launch would take place as part of the planned artillery drills.
"The hypersonic weapon will not be used in the context of these exercises," Gladkiy said. "There is no hidden meaning in the exercises that we are performing today."
Russia's TASS news agency reported earlier this month that a frigate participating in the drills would perform a training launch of the Zircon missile during the exercise.
A Russian frigate armed with the Zircon weapon system has been deployed to the joint exercise.
Along with the Avangard hypersonic glide vehicle which entered combat duty in 2019, the Zircon forms the centerpiece of Russia's hypersonic arsenal. President Vladimir Putin has called it "unstoppable."
South Africa has defended its decision to host the Mosi II naval exercise despite the concerns of diplomats from European Union and NATO countries.
"There is a difference between military and politics," Lieutenant-General Siphiwe Sangweni, chief of joint operations in the South African National Defense Force, told a news conference in Richards Bay.
He said the army was "guided by government" but also needed to learn skills from other military forces to protect South Africa and for use in international peacekeeping operations.
"Yes, there will be other countries who feel differently in how we have approached this, but... all countries are sovereign nations and have a right to handle things (as) they see fit," he said.
Sangweni said "cooperation and coordination with all other militaries is one that is very important to us".
South Africa's governing African National Congress has been historically close to Moscow, which supported its struggle against a racist apartheid regime that many Western states considered a Cold War ally.
Domestic critics of its relationship with Russia, however, warn that maintaining those warm ties in the wake of Moscow's invasion of Ukraine risks damaging relations with major Western trading partners.
This report was sourced from Reuters and Agence France-Presse.