IT officials said Rs 9 crore cash was recovered from the search of various properties linked to the minister, who has been taken to his house in Bengaluru from the resort by the IT team.
Note counting machines have been brought at a location in Safdarjung Enclave in Delhi and in Hasan and Mysuru in Karnataka to count the cash.
The minister, who was in charge of the 44 MLAs lodged there to prevent the BJP from allegedly "poaching" on them, was at the resort when the search took place, IT officials said.
As the raids on the resort triggered angry reactions from the Congress, the IT department said the resort is not being raided.
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They said only the minister's room in the resort was "searched" and not of the MLAs from Gujarat.
Senior Congress leader Ahmed Patel, who is contesting the Rajya Sabha polls from Gujarat, slammed the I-T raids on the Karnataka Energy minister and accused the BJP of indulging in an "unprecedented witch-hunt" to win one Rajya Sabha seat.
IT officials said a total of 39 premises of the minister and his family are being raided by a team of about 120 Income Tax Department officials with the aid of central paramilitary forces. The raids are taking place in Delhi and Karnataka.
The IT Department further said the timing of the search was decided well in advance.
"The events involving certain MLAs of another state being brought to Karnataka were unforeseen and unpredictable events," it said.
"The search under Section 132 of the Income Tax Act is an evidence gathering exercise which is being carried in compliance with all statutory requirements. The search is the continuation of an investigation which has been in progress for a considerable period of time," the IT department said.
The Congress legislators have been camping at the resort since Saturday last after the party flew them in here to fend off alleged "poaching" attempts by the BJP ahead of the August 8 Rajya Sabha polls in Gujarat.
Six of the 57 Congress MLAs in Gujarat, from where senior party leader Ahmed Patel is contesting for the Rajya Sabha, have resigned from the party in the last few days with three joining the BJP on Friday.
The MLA are attending classes on a host of topics including "the party's achievements in the last 60 years" and "the BJP's lies" among others, since yesterday.
The move to hold the classes came at a time when a few MLAs from flood-hit constituencies of Gujarat had reportedly expressed their intention to go back, worried about the public opinion going against them.
Earlier, the itinerary during their stay here included visit to some tourist destinations and religious places, which drew criticism as MLAs were accused of "abandoning" voters when their constituencies were facing nature's fury.