According to reports, Thakur, who went on leave last week, had sought to be relieved from the Ministry.
A 1996 batch IPS officer of Rajasthan cadre, Thakur was appointed as private secretary to the HRD Minister in September last year.
She had replaced Vinita Srivastava, a Railway Engineering Services (RES) officer, who had a brief tenure as Irani's PS after she assumed charge of the ministry in May last year.
Now, the name of M Imkongla Jamir, a 2002 Karnataka cadre IAS officer, is doings the rounds as Thakur's replacement in the Ministry.
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Radha S Chauhan, Joint Secretary, Secondary Education, joined UIDAI a couple of months back much before completing her five-year tenure at the HRD Ministry.
Other officers such as Veena Ish, Jagmohan Raju and Praveen Prakash had sought early transfers from the ministry.
In April this year, Amarjeet Sinha, Additional Secretary in the Ministry, who had supposedly developed differences with Irani, was transferred to the Rural Development Ministry.