The cash payments were made personally by V Mulgund to the AICC, the department alleged.
"Rs 3 crore were personally delivered by Mulgund to AICC office on January 1, 2017. On January 9, another Rs 2 crore was delivered. These unaccounted monies were delivered on the direction of Shivakumar and Sunil Kumar Sharma, another accused," it said.
In the complaint, the I-T has accused Mr Shivakumar and Mr Sharma of transporting huge amount of unaccounted cash on a regular basis through 'hawala' channels with help of three other accused.
Other accused are Sachin Narayan, Anjaneya Hanumanthaiah and N Rajendra, it said.
According to the I-T, Sachin Narayan is a business partner of Mr Shivakumar and Mr Sharma is the proprietor of Sharma Transports, which runs a fleet of luxury and passenger buses and provides transport services to various concerns and individuals on rental basis.
Mr Haumanthaiah is an employee at Karnataka Bhavan in New Delhi, allegedly responsible for storing and handling unaccounted cash of Shivakumar in Delhi, it said in the complaint.
Rajendra is a caretaker of Karnataka Bhavan and works for Mr Sharma, besides looking after immovable properties of Shivakumar and Sharma, it said.
The I-T department alleged that all five accused conspired to evade tax.
He was involved in organised tax evasion as part of conspiracy by engaging others, the department said.
Various material such as diaries and loose sheets with entries running into crores of rupees of unaccounted transactions as the per statement of N Rajendra,one of the five accused, were seized during the raids, it said.
Meanwhile, the Special Court for Economic Offences has registered a fresh criminal case against Mr Shivakumar for "wilfully" trying to evade tax and filing "false" income tax statement.
Mr Shivakumar has alleged that the IT department was targeting him and not letting him breathe but he would fight the case legally.
To a question whether it was politics of vendetta, he had told PTI yesterday, "You write whichever way you like. Assess it. They are not letting me to breathe. I don't know why only me."
He had warned those trying to "fix" him, saying he too has enough "evidence and documents" against his rivals.
Deputy Chief Minister and state Congress chief G Parameshwara today flayed BJP for misusing central agencies for targeting their rivals for political gains. "The BJP is targeting their rivals through agencies like I-T, but it will not be effective. I will give a fitting reply to it," he said.
Chief Minister H D Kumaraswamy has said govermment would stand by Mr Shivakumar if he has not done anything illegal.
"If things are legal, we will stand by (Shivakumar). ...let there be no doubts on that," Mr Kumaraswamy said yesterday in response to a question whether the government would stand by Mr Shivakumar.