Her are some references to the departmental or district status of the Indian Territory. Looks as if others were confused as well:

http://digital.library.okstate.edu/chronicles/v017/v017p147.html
Chronicles of Oklahoma
Volume 17, No. 2
June, 1939
FORT DAVIS
By Grant Foreman1
Page 148
In November 1861, the Confederate government created the department of Indian Territory, and named Brigadier-general Albert Pike to the command of that department [Nov 5]

http://www.tsha.utexas.edu/publications/journals/shq/online/v021/n3/article_3.html
Southwestern Historical Quarterly Online
volume 021 number 3
[extract]
THE POWERS OF THE COMMANDER OF THE CONFEDERATE TRANS-MISSISSIPPI DEPARTMENT, 1863-1865
FLORENCE ELIZABETH HOLLADAY
1. The Organization of the Trans-Mississippi Department

At first the territory west of the Mississippi was divided into several departments; then it became a district, the Trans-Mississippi, of the Western Department. Official Records, War of Rebellion, Series I, Vol. VII, 826. n164.This district was too large for effective administration, however, and in May 1862, it was erected into the Trans-Mississippi Department, which was composed of the districts of Arkansas and Texas. The Arkansas district, which included Arkansas, Missouri, and that part of Louisiana lying north of the Red River, was placed under the command of Major General T. C. Hindman; while the Texas district, consisting of Texas and the remainder of Louisiana west of the Mississippi River, was assigned to Major General P. O. Hébert. Off. Recs., IX, 713; General Orders No. 1, [Hébert] June 18, 1862, ibid., 719. n165
There was strong objection in Louisiana to this arrangement since it divided the state between two districts and gave it adequate protection in neither. The protests which were made to the President by state officials Off. Recs., LIII, 819.n166 and the steady advance of the Federals on the Mississippi probably led to the next change. In July Major General T. H. Holmes was sent to command the Trans-Mississippi Department. He made Louisiana a separate district and assigned Major General Richard Taylor to command it. The Indian Territory was added to the Arkansas District and Arizona and New Mexico to that of Texas. ibid., IX, 731. n167

http://www.vinnysa1store.com/nativeamericancivilwar4.html
THE AMERICAN INDIAN AS PARTICIPANT IN THE CIVIL WAR
BY
ANNIE HELOISE ABEL, Ph.D.
Professor of History, Smith College

[extracts]
BALDWIN, June 5, 1862.
(Received 6th.)
THE PRESIDENT:
Do not send any one just now to command the Trans Mississippi District. It will bring trouble to this army. Hindman has been sent there temporarily. Price will be on to see you soon.
EARL VAN DORN, Major-General.
[Ibid., vol. lii, part 2, supplement, p. 320.]]
Hindman had assumed the command of the Trans-Mississippi
Department.[321] As an Arkansan, deeply moved by the misfortunes and distress of his native state, he had stepped into Van Dorn's place with alacrity, intent upon forcing everything within his reach to subserve the interests of the Confederate cause in that particular
part of the southern world. To the Indians and to their rights, natural or acquired, he was as utterly indifferent as were most other American men and all too soon that fact became obvious, most obvious, indeed, to General Pike, the one person who had, for reasons best known to himself, made the Indian cause his own.
General Hindman took formal command of the Trans-Mississippi
Department at Little Rock, May 31. It was a critical moment and he was most critically placed; for he had not the sign of an army, Curtis's advance was only about thirty-five miles away, and Arkansas was yet,in the miserable plight in which Van Dorn had left her in charge of Brigadier-general J.S. Roane, it is true, but practically denuded of
troops. Pike was at Fort McCulloch, and he had a force not wholly to be despised.[322]
It was to him, therefore, that Hindman
[Footnote 321: _Department_ seems to be the more proper word
to use to designate Hindman's command, although _District_ and
_Department_ are frequently used interchangeably in the records.
In Hindman's time and in Holmes's, the Trans-Mississippi Department was not the same as the Trans-Mississippi District of Department No.2 [See Thomas Jordan, Chief of Staff, to Hindman, July 17, 1862,
_Official Records_, vol. xiii, 855]. On the very date of
Hindman's assignment, the boundaries of his command were defined as follows: "The boundary of the Trans-Mississippi Department will embrace the States of Missouri and Arkansas, including Indian Territory, the State of Louisiana west of the Mississippi, and the State of
Texas."--Ibid., 829.]
[Footnote 322: Yet Hindman did, in a sense, despise it and, from the start, he showed a tendency to disparage Pike's abilities and efforts. On the nineteenth of June, he reported to Adjutant-general Cooper,
among other things, that he had ordered Pike to establish his headquarters at Fort Gibson and added, "His force does not amount to much, but there is no earthly need of its (cont.)]
made one of his first appeals for help and he ordered him so to dispose of his men that some of the more efficient, the white, might be sent to Little Rock and the less efficient, the red, moved upward "to prevent the incursions of marauding parties," from Kansas.[323]
The orders were repeated about a fortnight later; but Pike had already complied to the best of his ability, although not without protest[324] for he had collected his brigade and accoutered it by his own energies
and his own contrivances solely. Moreover, he had done it for the defence of Indian Territory exclusively.

http://www.answers.com/topic/trans-mississippi-theater-of-the-american-civil-war
Trans-Mississippi Department
The Confederate Trans-Mississippi Department was formed May 26, 1862, to include Missouri, Arkansas, Texas, Indian Territory (now Oklahoma), and Louisiana west of the Mississippi River. It absorbed the Trans-Mississippi District (Department Number Two), which had been organized January 10, 1862, to include that part of Louisiana north of the Red River, the Indian Territory, and the states of Missouri and Arkansas, except for the country east of St. Francis County, Arkansas, to Scott County, Missouri. The combined department had its headquarters at Shreveport, Louisiana, and Marshall, Texas.

Arkansas in the War Between the States
http://asms.k12.ar.us/armem/welch/TIMELINE.HTM
............Beauregard appointed Major General Thomas C. Hindman to succeed Van Dorn as commander of the Military District of the Trans-Mississippi. Hindman declared martial law, and using draconian methods, raised and equipped a small army, headquartered in Little Rock.........................

University of Arkansas Libraries
Manuscript Resources for the Civil War
40. Confederate States Army. Trans-Mississippi Department.
General and special orders, 1862-1865; 6 rolls.
The Trans-Mississippi Department was established in May 1862 and included territories which were formerly designated as the Trans-Mississippi District. Some of the records of both the District and Department are intermingled as a result

http://www.csawardept.com/history/armies/
Janurary 1862
Trans Miss District-Maj Gen Van Dorn Jan 29-May 26, 1862
Subsection of Dept No 2

1/10/62 embraced the part of Louisiana north of Red River, the Indian Territory west of Arkansas, and states of Arkansas and Missouri..........
5/26/62:Merged into the Trans-Miss Dept.