Raids were conducted at the office of Hyderabad Karnataka Education Society, which runs a string of institutions, including medical and engineering colleges across the state, particularly in north Karnataka, official sources said.
The residences of former member of legislative council Sashil G.Namoshi, who is heading the institution, and some members of the Society Committee were also raided, the sources said.
The places raided in Bangalore include Saptagiri College at Hesarghatta and Ambedkar College at DJ Halli, officials said.
Office of the BGS Education trust, run by the powerful Adichunchanagiri Mutt here in whose complex it is located, also came on the radar of IT officials, which drew condemnation from some political leaders.
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IT department said the raids were "routine".
Former Chief Minister and BJP leader D V Sadananda Gowda said he did not understand why religious institutions doing social service were being targetted, adding, it was "not a good sign."
State Congress leader D K Shivakumar also flayed the raid on Adichunchanagiri trust, saying he would take up the issue with the government.