CBI sources said the searches took place at the office of Nikunj Aggarwal, OSD to Jain and Anup Mohta, Director Chacha Nehru Bal Chikitsalya.
They said the teams have gone to the offices of Aggarwal and Mohta to get records related to appointment and other allegations including Aggarwal's nomination for a course at IIM Ahmedabad and for a trip to Bejing, China.
The sources said the team also spoke to Aggarwal in his office.
CBI had earlier registered an FIR in connection with alleged irregularities in the appointment of Aggarwal, as OSD to Jain.
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The agency registered the case on the basis of a complaint from Delhi government's Deputy Secretary Vigilance K S Meena. The complaint is now the part of the FIR.
The FIR is against Mohta and Aggarwal, for alleged criminal conspiracy and under provisions of the Prevention of Corruption Act.
In its complaint, the vigilance department has claimed Aggarwal was appointed as Senior Resident (Ortho) in Chacha Nehru Bal Chikitsalya on ad hoc basis on August 10, 2015 even though there was no proposal to engage an SR and no such post was available.
"Also no advertisement was issued by the hospital for the selection of Dr Nikunj Aggarwal as SR. No walk-in interview was conducted for the purpose," it alleged.
Aggarwal had made a handwritten application on a "plain paper" for appointment in the hospital on August 6, 2015 and within four days his appointment was approved without following any procedure, the complaint alleged.
A senior government official said that it is the prerogative of the minister to appoint his OSD and that there was no irregularity adopted by the government while appointing Nikunj Aggarwal.
"Since October, he has not been holding any official post in the Delhi government as Health Minister Satyendar Jain had discontinued his service. Aggarwal had been appointed on contractual basis," the official said.