In the notice, issued on Friday, the BMC has asked the bungalow owner to show 'sufficient cause' within seven days as to why such alterations should not be removed.
Earlier, the Mumbai civic body had also issued a notice to Rane's 'Aadhish' bungalow over alleged unauthorised construction and rejected his proposal for its regularisation.
The project involves development of a military-civil, dual-use airport; international container trans-shipment terminal; a gas, diesel, and solar-based power plant, and a township.
The environment ministry on Thursday gave its nod to a plan for constructing a grand statue for Maratha warrior king Shivaji in the Arabian Sea off the coast of Mumbai.
Environment ministry also plans to cut the two-stage mandatory clearances under the Environment Protection Act to a single stage, shaving six months from the process.
The allegation against Khan is that he had applied to purchase the agricultural land for farming but constructed a farmhouse for personal use instead.
India loses 333 acres of prime forest every day. Instead of working to conserve India's forests and water resources, the environment minister has set up a committee to 'dismantle' the five key laws that provide environmental protection.