He also alleged that Waikar has made an additional construction in the state-run gymnasium located adjacent to the "grabbed" land and is running the facility through his private unregistered trust.
Demanding ouster of the minister, Nirupam said an FIR should be registered and the "usurped" land taken back by the government.
"Aarey Milk Colony's CEO has been sending letters to Mhada (Maharashtra Housing and Area Development Authority) to demolish the illegal part of the structure in the gymnasium for over a year. However, as Waikar is minister of Housing, he is misusing his influence and the structure has not been razed so far," Nirupam claimed.
Addressing reporters, Nirupam said the minister has put barricades around the 20-acre land worth Rs 20 crore and is planning to construct a 'Matoshree'-like structure there.
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'Matoshree' is the residence of Shiv Sena chief Uddhav Thackeray at Kalanagar in suburban Bandra.
"This is very strange (given) that Shiv Sena is against the proposed car-shed for Metro-3 project in the green zone of Aarey Colony.
"Sena's own minister has not only made illegal structure in that zone, but has also usurped the 20-acre vast tract of land. This is not only a huge scam and a perfect case of the conflict of interest, but also a criminal conduct on behalf of the minister," Nirupam told the press conference.
Nirupam, a former MP, said he would write to Chief Minister Devendra Fadnavis and Lokayukta about the "land scam".
"I will ask Fadnavis to sack the minister immediately from his Cabinet," he added.
He alleged that Fadnavis is "patronising" corruption.
"I have least hope from the Chief Minister to act against the tainted ministers like in other cases. This CM is using his full energy to protect the tainted ministers of his government. I am going to burn his effigy near his residence in coming days as he (Fadnavis) has become the patron of corruption," he alleged.
Meanwhile, Waikar has rubbished the charges terming them as "politically-motivated".
"Every rule and regulation has been followed in the construction of the gymnasium, (besides) due permission was taken from the Collector. The allegations levelled against me by Nirupam are politically motivated and are being made eyeing the (upcoming) elections to BMC (Brihanmumbai Municipal Corporation), " Waikar told