Nirupam had alleged that Waikar grabbed 20 acres of land in Aarey Colony area here and illegally constructed a gymnasium and a building containing 40 rooms there.
Waikar, a Shiv Sena leader, said the probe by Lokayukta didn't find any irregularities in the construction.
The minister also alleged that because of Nirupam's "reckless behaviour", many senior Congress leaders had distanced themselves from the party.
He had sent a legal notice seeking an apology from Nirupam, Waikar said, claiming that "my political rivals are targeting me through Nirupam".
The Congress leader, however, stuck to his allegations.
"The Lokayukta hasn't given Waikar a clean chit. Lokayukta could not probe the allegations because of a technical reason," Nirupam claimed.
After getting copy of the Lokayukta's order, he will move the High Court, Nirupam added.
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