The house is located close to the office of Delhi Police's Security Wing.
S Suresh Kumar, secretary to Naidu, is in the US for higher studies and the house has been unoccupied for a year, police said.
The burglary happened on March 31 and it was the driver V Kuttan Pillai, who informed police about the burglary.
"Since Kumar is not in India, it is still not known what valuables were taken away by the accused. Kumar has gone to the US for a year-long course. It appears that a large amount of cash and valuables were not kept at home," said a senior police officer.
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Kumar's driver Pillai stays in the servant quarters and informed police after he saw that the house had been ransacked. He informed Kumar and made a PCR call.
Forensic teams analysed the spot and police is scanning the CCTV footage from the adjoining areas to gain clues to the accused.
Kumar's house didn't have any CCTV cameras installed so police do not know at what time the incident happened.