Separate Central Bureau of Investigation (CBI) teams conducted searches at more than 17 locations in Chennai, Karaikudi, Delhi and Noida besides Mumbai and Gurugram.
After the raid at his residence, Karti was seen getting into a vehicle along with CBI officials, who then took him to his office also located in Nungambakkam.
The five secretaries who constitute the FIPB, the officials of the FIPB secretariat and the competent authority in each case are public officials, Chidambaram said, adding that there was no allegation against any of them.
DMK working president M K Stalin accused the Centre of "misusing" agencies like CBI and said the former union minister and his son would face the matter legally.
"I mean.(this is) absolute nonsense", Chidambaram told reporters adding he was not in Chennai.
In turn for the favour, INX Media transferred money to several companies, directly or indirectly controlled by Mr Karti, the agency alleged.
"The CBI raid is a political witch-hunt and conspiracy by the government and the opposition members will not be silent over the issue", Congress party spokesman Randip Singh Surjewala said.More news: Syria activists say civilians killed in strike on IS village
The INX media was owned by the former media man, Peter Mukerjea who has been jailed for the alleged killing of Sheena Bora along with Indrani Mukerjea.
According to an NDTV report, the raids are linked with the allegation that Karti Chidambaram's company facilitated clearances for foreign investment to a media company in 2008 for kickbacks.
The raids were "in connection with criminal misconduct" in granting approval for foreign investment deals, a CBI spokesman said without giving further details.
P. Chidambaram has been named in a police complaint in the INX deal, which accuses his son Karti of receiving "consultation charges" after the INX Media won government approval to receive foreign investments. "The source informs that the very reason for getting the invoice raised in the name of of APSCL for the services rendered by Chess Management Services was with a view to hide the identity of Karti Chidambaram", reads the FIR.
"There is a long history to these proposals (of INX Media and INX News)". FIPB Unit had in its report clearly mentioned that there was an inflow of Foreign Direct Investment to the tune of Rs 4.62 crore. The company, on the advise of FIPB officials, filed fresh request which was cleared by the Finance Ministry and the Finance Minister. But contrary to the conditions of approval, the company deliberately made a downstream investment to the extent of 26 per cent in its capital.
Finance minister Arun Jaitley asserted that the CBI and the income tax department had acted on the basis of "substantial basis and reasonable suspicion".