Johor Zoo manager Zakaria Rosli said there was no truth in the report which had also been posted on the YouTube, titled "Wildlife for sale at Malaysia zoos" recently.
The zoo is the only one in Malaysia run under the administration of the state government.
An Al-Jazeera journalist and a cameraman were said to have entered the zoo on March 13.
They made their way to the exotic animals private exhibition centre within the zoo compound through its back door.
The centre's worker Mohd Yusof Salee said the journalist made her way into the exhibition centre about 10am.
"We were closed on that day, but she claimed that they were heading for Kuala Lumpur and did not want to miss the chance to see the animals.
"So, we allowed them in after paying the RM1 entry fee."
Yusof said as the only person at the centre who could speak English was a Bangladeshi worker, Abdul Rahim Abdul Matin, who is in charge of pony rides.
The reporter and cameraman was referred to Rahim.
"The journalist repeatedly asked whether she could buy a few of the 10 protected species in the enclosures, but was told that she could not as this was against the law. She was told that the animals were not for sale."
"Rahim, however, did tell her that if he was not wrong, RM300 was the estimated sum required to obtain a permit to keep a monkey as a pet.
"He was not referring to the wild cat and white gibbon in our enclosures as shown in the Al-Jazeera's footage."
"That part where Rahim said RM300 was the estimated cost for the permit, however, was not shown in the footage."
"The footage was edited in such a manner that it did not show and tell the correct story," said Yusof when met at the zoo.
Zakaria, meanwhile, said the private centre was leased out to a private exhibitor since 2006.
"He (the exhibitor) is in charge of the snakes. At the back of the centre, there are about 10 protected species like the civet, birds, slow morris, gibbons, squirrels and monkeys.
"The animals in his closures belong to the Johor Zoo.
"They are housed in the cages and the exhibitor has been using them with the permission of the zoo management for educational exhibitions in schools."
Also shown in the Al-Jazeera footage was a privately-run zoo in Saleng, Kulai.
According to the report, the Malaysian Wildlife and National Parks Department (Perhilitan) had, on numerous occasions, raided the zoo and seized several protected species kept without permits.
The department's enforcement director Saharudin Anan said the proprietor's house was raided following the report and several protected animals were seized.
Saharudin said there were 10 wildlife-related charges pending against the man."