The job went to the company of Thabo Mokoena, previously a special adviser to then mineral and energy affairs minister Phumzile Mlambo-Ngcuka, who is now deputy president.
City manager Wallace Mgoqi said: "A view was taken at administrative level that in the nature of things, for phase one of the project, it was going to be a closed bid, having regard to the intimate knowledge and networks TM Consulting had on the project."
Independent Group of newspapers reported earlier that the consultancy was charging the city R1 200 an hour for project direction and R1 000 an hour for a development co-ordinator.
Mgoqi said the project was "the brainchild of the department of minerals and energy (DME)".
"It is so that Thabo Mokoena was then an adviser of the then minister at the DME," he said.
"The concept was brought to the City of Cape Town by TMC Consulting and presented to the mayoral committee which gave its approval for the African Jewellery City to be established so as to take advantage of local manufacturing and beneficiation in minerals produced in this country."
Mgoqi said the first, non-tender, phase involved "putting the concept together", doing feasibility studies and identifying land.
The second phase, which had been put out to tender, would involve identifying a developer who would be responsible for the actual construction and implementation of the project.
He said phase one "establishment costs" would be fully recoverable "within this financial year" from the successful developer.
These funds would revert to the city budget to be used for service delivery.
The Democratic Alliance earlier queried Mokoena's appointment, saying his consultancy, on the face of it, brought no specific expertise to the project.