Mathur, the sources claim, has links with an influential business house and it seems that the normal procedure of going through the department's promotion committee was not adopted while announcing his promotion.
Unless the government addresses the fundamental technical flaw in its decision the disquiet in India's external intelligence agency will not go away.
R&AW chief K C Verma is reportedly trying to douse the fire by saying that R&AW service cadre and Indian Police Service cadre officers should and will have to work in harmony within the organisation.
Mathur, who had the rank of additional secretary before his promotion to special secretary, is an IPS officer of the 1975 batch from the Manipur cadre.
His promotion affected six officers above him, who will now be entitled to remuneration less than Mathur: P Heblikar, C K Sinha and Bidhan Rawal of the 1973 batch and Sharad Kumar, Anand Arni and Ashok Kapur of the 1975 batch. Some of these officers are said to have gone on leave.
Sources say one of Mathur's close friends since their days at Lucknow University is a senior corporate executive. Mathur has had two postings abroad: He was posted in Brussels and later to Pakistan during 1995 to 1998.
After his Pakistan posting Mathur was sent to the Intelligence Bureau and posted at Guwahati.
When M K Narayanan became India's national security adviser, Mathur returned to R&AW, where he handled two neighbouring countries.
Sources claim that some officers, affected by Mathur's promotion, will be promoted soon. Heblikar has been appointed special secretary.
While the government hopes the controversy will die down soon, Mathur's promotion puts him on track for the R&AW chief's post when Verma retires in 2011.