The work to renovate the 153-year-old Gothic Revival architecture was given to the Indian National Trust for Art and Cultural Heritage (INTACH) by the civic body in September 2016.
However, the heritage organisation stopped the work last year after it faced some financial hurdles.
The renovation work is set to resume soon as the BMC has allotted the funds to INTACH as per the bills raised by the body, according to a civic official.
However, the decision on the interest waiver, demanded by the INTACH, would be taken by the civic commissioner.
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"The body had also sought an interest waiver on the payment made by us as the mobilisation advances. Since they have sought a special concession, this mater will be forwarded to the BMC commissioner who will take the final decision," Shirsath added.
With the INTACH and the BMC having sorted out the issues, it is now hoped that the work would be completed soon.
Noted architect Vikas Dilawari, who is overseeing the restoration project on behalf of the BMC, said they are hopeful that the project would be completed within two months after the work is restarted.
"There were some glitches which have almost been resolved and we hope to complete the project in two months after resumption of the renovation work. The Flora Fountain, a monument that has stood testimony to the city's history for over 150 years, will get refurbished soon," he told PTI.
Another BMC official, attached with the renovation of the project said, "We have applied latest technology to restore the pride of this historical piece. We have applied high-density steam to remove the coat of murk. This is the least invasive technique with long-term benefits, as there is no use of chemicals".
Flora Fountain, at the Hutatma Chowk, is an ornamentally and exquisitely sculpted architectural heritage monument located in the Fort business district in the heart of South Mumbai.
Hutatma Chowk square that hosts Flora Fountain was officially renamed in 1960 in memory of the members of Samyukta Maharashtra Samiti, who lost their lives when police fired upon their peaceful demonstration. A statue of a "Martyr with a Flame" stands next to Flora Fountain.