Sources said the Delhi government, upon direction from the LG's office, sent a letter to CBI earlier this month to look into the matter.
Reacting to the development, Jain rejected the allegation of favouritism saying she had worked voluntarily and not a single paisa was given to her.
In July, Soumya had resigned the post of adviser of the Aam Aadmi Mohalla Clinics following Opposition's allegation of nepotism, though the Health Minister had been maintaining she was not being paid a "single penny".
Meanwhile, senior BJP leader Vijender Gupta said recommendation of the matter to CBI by the LG office "strengthens the belief that the AAP government "indulged in gross irregularities in the matter of appointments".