Chief maritime strategy director Bernhard Hein Teuteberg said the navy was prepared to deal with this threat.
The key to fighting pirates was collective Southern African Development Community (SADC) security, he said.
Teuteberg was briefing reporters in Simon’s Town, Cape Town, on the state of the navy.
“We have proposed a maritime zone and regional maritime domain zone centres, all working together to exchange information.”
Information about vessels moving around South Africa would start being centralised on a system from April 1. This information would hopefully be shared with centres in the region.
South Africa formalised diplomatic ties with Somalia on Wednesday, which would likely help anti-piracy efforts.
Mozambique, Tanzania and South Africa had also been working together for the past year to secure the channel between the mainland and Mozambique.
Under “Operation Copper”, a frigate and a helicopter, special forces and a maritime squad had been deployed.
Mozambique was providing a naval base in Pemba at no cost, and 12 inland control vessels, to protect the lagoon and area around the base.
Three Tanzanian vessels were patrolling inshore areas around Dar es Salaam, and between Mozambique and Tanzania.
Beaches in hot spots were being patrolled on foot, and local communities were ready to report any suspicious activity.
Teuteberg said once pirates were arrested it could be difficult deciding who dealt with their criminal prosecution.
“It would be potentially unwise to do the trials and incarcerations of pirates here [in South Africa]. We believe [though that] there should be a single point where these trials happen.”