Mr Mehta has been under fire ever since he allegedly allowed "unauthorised" transfer of extra building rights in the SRA (Slum Rehabilitation Authority) project at the MP Mills Compound in south Mumbai, originally granted to slum dwellers, to project-affected people.
The opposition has been alleging that the move was aimed at favouring a particular developer.
"After I dug deep into the MP Mills compound issue, there were many skeletons that were unearthed and I asked myself if this was another 'Adarsh' (referring to the Adarsh scam),"
Mr Fadnavis said replying to a motion moved by Leader of Opposition Dhananjay Munde in the Legislative Council.
He said said all permissions for construction on this particular land were given between 1999-2004. "As per the property card, that land is owned by the Defence Ministry. How could the previous government permit an additional FSI on the plot when it was known that it was defence land," he said.
Mr Mehta had wrongly mentioned on the file of the project that he had kept the chief minister in loop about the transfer, which was denied by Mr Fadnavis.
"I have decided to conduct a probe by the Lokayukta into the allegations made by the Opposition against the Housing minister, even though there was no decision taken in this particular case," he said.
The opposition has been raising the pitch for Mr Mehta's resignation and had repeatedly stalled the proceedings during the monsoon session of the state legislature over the issue.
The Opposition had also accused Mr Mehta of incorporating the names of his family members as the beneficiaries of a slum redevelopment project in suburban Ghatkopar.
Meanwhile, on allegations against Industries Minister Subhash Desai of Shiv Sena, Mr Fadnavis said the government will request the Lokayukta to consider the case.
The opposition had alleged that Mr Desai had illegally denotified MIDC land within two years.
"Out of 16,909 hectares of denotified land, 9,335 hectares were denotified by the previous government and only the notification has been issued by the present dispensation.
This government has denotified only 7,734 hectares of land," Mr Fadnavis said.
"We will request the Lokayukta to consider this case as well, but if this doesn't work out, then we will conduct an independent inquiry," he said.
The chief minister said mere denotification of land by any government does not mean that corruption has taken place.
"Nonetheless, we will probe if land was denotified to favour builders or for some other reason. There will be a fair and an independent report conducted. We will table the report of both the probes in the House," he said.
In his reply, Mr Munde said, "Fadnavis is highly skilled in trying to confuse members of the Opposition and that nobody has the capability to match the CM's expertise".
Regarding the allegations of graft against IAS officer Radheshyam Mopalwar, who was recently removed as managing director of the Maharashtra government undertaking MSRDC, the CM said a joint SIT, consisting a serving IAS officer and officials of the Economic Offences Wing, will be formed and a probe will be conducted.