Mathew sent a letter to Chief Minister Ashok Gehlot Wednesday, requesting he be allowed to go on leave till the assembly elections are held in Rajasthan.
Polling in the state is scheduled for Dec 1.
"He was to withdraw the leave application, but as he did not budge from his decision, Chief Minister Gehlot accepted his request and allowed him to go on leave," said a senior officer at the chief minister's office.
The Bharatiya Janata Party's state unit on Oct 15 accused Mathew of "deliberately working in favour" of the ruling party.
BJP leaders handed over a memorandum to the chief electoral officer about Mathew's "questionable way of functioning".
The officer of the CM's office said that in an emotionally-charged letter, Mathew had stated that he was hurt by the allegations being levelled against him.
In the letter, he stated that he has been rendering his duty with full devotion and commitment since 1977.
Mathew went on to say that during his entire career he worked wholeheartedly to implement policies and programmes of every government but was never accused of being partial.
"He had stated in the letter that he was going on leave to guard his self-respect. Chief Minister Gehlot, respecting his sentiments, granted the leave," said the officer.
He added that the state government will send a panel of names of three senior most Indian Administration Service (IAS) officers to the election commission for appointment as acting chief secretary.
"The election commission will appoint one of them as the acting chief secretary till Mathew returns from leave," said the officer.
--IANS (Posted on 19-10-2013)