Till 1950, the audit of North Eastern Railway had been entrusted to this office headed by Dy. Chief Auditor under the administrative control of the Chief Auditor for O.T. Railway and E.P. Railway with Headquarters at New Delhi. A Chief Auditor was independently posted in this office in 1952. The designation was changed from Chief Auditor to Director of Audit w.e.f. 01.04.1979 and Principal Director of Audit w.e.f. 01.03.1990. Presently this office is headed by the Director General of Audit since July 15, 2019.

As a result of re-organisation in January, 1958, the North Eastern Zonal Railway System was bifurcated in two viz. North Eastern Railway and North East Frontier Railway with Headquarters at Gorakhpur and Pandu (Guwahati) respectively. "Divisional System" was introduced in this Railway in May, 1968 resulting in creation of four Divisional Audit Offices at Izatnagar, Lucknow, Samastipur and Varanasi in August, 1969. The fifth Divisional Audit offices at Sonepur came into existence in 1978. In addition to the above, there were three Workshops and Stores Audit Offices in Izatnagar, Samastipur and Gorakhpur and a Broad Gauge Construction Audit Office at Gorakhpur. The NER, under its audit jurisdiction have 486 stations and 3,450 Kms of Track.

On 1st October, 2002, Sonepur and Samastipur Divisions of North Eastern Railway were merged with the newly created zone i.e., East Central Railway having its headquarter at Hajipur.

Presently, North Eastern Railway has three Divisions at Varanasi, Lucknow and Izatnagar with headquarters at Gorakhpur. This Railway, being a passenger oriented system, provides reliable transportation facility to the people of Uttar Pradesh, Uttarakhand and Western Bihar and also gives impetus to the socio-economic and cultural development of the region. This Railway also caters to the transportation needs of neighbouring country Nepal.

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