"A permit to destroy the crocodile had recently been issued following numerous failed attempts to catch it alive. Attempts to catch it lasted for more than four years," spokesperson Musa Mntambo said in a statement.
The crocodile was shot around 13:45 following a call from someone who saw the crocodile outside the river.
"Over the years, the crocodile had become 3m long. It had begun bothering dogs along the banks of [the] river," said Mntambo.
"It was also posing a danger to people using the river. Kayaks are used on the river on a daily basis and people also use the river for fishing."
He said killing the crocodile was done as a preventative measure, as authorities believed it was only a matter of time before the crocodile attacked a person.
It was not known why the crocodile had chosen to live in the section of river it inhabited, since the area was industrial in nature.