The case pertains to 2013 and 2017, during which Chohan Doley served as Labour Commissioner twice.
Mr Doley, at present the panchayat and rural development secretary, was arrested by the Chief Minister's Special Vigilance Cell (SVC).
"We have arrested Mr Doley for misappropriation of funds under the Vigilance Case No 9/2017. The scam is estimated at Rs 121 crore and it took place from 2013 to 2017," SVC SP Khanindra Kumar Choudhury told PTI.
The case is related to awarding contracts to a private firm for printing leaflets, folders and other such materials of the labour department during the said period, he added.
"Mr Doley was admitted in Down Town Hospital. We picked him up from there, brought him to our office and arrested him. We will produce him before the court," Mr Choudhury said.
"Further investigation is on. At this point of time, we cannot say anything more," he added when asked about possibility of more arrests in the coming days.
In one of the biggest crackdown against corruption in recent times, the SVC has arrested 22 civil services officials in last six days in connection with the cash-for-job scam in the Assam Public Service Commission (APSC) and is looking for three more officials, who are evading arrests.
On November 7, Directorate of Information & Public Relations Director Ranjit Gogoi was arrested by the SVC for an alleged Rs 32-crore scam in putting up of publicity hoardings of government schemes during Congress regime.