The bench, headed by Chief Justice Mohit Shah, gave the direction in response to a public interest litigation filed by Monica Mathani, a city resident.
The court has sought replies by October 24.
According to Mathani, the project violates several safety norms. For instance, the PIL says, while the latest rules mandate six metres open space around every building, the buildings adjoining the Metro network stand closer, which would make fire brigade vehicles difficult to move in if fire breaks out.