The event is scheduled to be held on January 21.
A bench led by Justice AS Oka also directed the BMC to consider the request of the organiser, Procam International, that it be allowed to put up stalls to serve water, energy drinks etc. to the participants.
Procam had approached the high court in September last year, alleging that the BMC was demanding an exorbitant fee for the marathon.
The petitioners have sought permission from the BMC to hold the day-long event and put up advertisements and hoardings across the city from January 15-21.
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Procam claimed that while last year, it had paid about Rs 26 lakh to the BMC for a similar event, this year, the civic body asked it to pay Rs 3.66 crore towards the "land fees, displaying advertisements and hoardings, and security deposit".
BMC counsel Ram Apte contended that it was a routine practice for the civic body to charge for the entire month, irrespective of the duration of such events.
"We have agreed to grant them permission for the event and advertisements and hoardings, subject to the condition that they pay us all the fees. The fee amount has been decided upon as per our valid rules and proper resolutions have been passed by the civic body for the same," he told the court.
"This is not a mere sports event, it has become a full fledged commercial activity. The organisers do not want any transparency," Apte claimed.
The bench however, directed that as an interim measure, the BMC must grant permission for the event if Procam paid Rs 1.05 crore -- Rs 79 lakh towards the rent of the land and Rs 26 lakh as security deposit -- by Monday (January 15).