BROOKVILLE, MISS., June 23, 1862.

General S. COOPER,

Adjutant and Inspector General C. S. Army, Richmond, Va.:

GENERAL: When I was relieved from the command of the Department of Alabama and West Florida and ordered by General Lee to report to General Beauregard at Corinth I supposed it was because General Beauregard has asked it, and that it was thought at the War Department that the service of an additional major-general were more needed at that time with the army at Corinth than to command the Department of Alabama and West Florida. It has occurred to me, however, that in that supposition I may have been, and probably was, in error, and that I was relieved from the command of the department because of some complaints made against me for the manner in which I had administered the department intrusted to my command.

I am induced to think that this may have been the case from the fact that on the 11th of April last Commander Farrand, Confederate States Navy, reported to the Secretary of the Navy that I had ordered two unfinished gunboats to be burned in Pensocola Bay on the 11th March, and the he could not discover the necessity for their destruction, and on the 12th of April the Secretary of the Navy communicated this report to the President, with the remark that, so far as he was advised, the destruction of those vessels was uncalled-for, and asked that I be called on to report why it was done.

My duties at the time were somewhat delicate and responsible and the performance of them calculated to give offence to many persons. Among other things I had to destroy much valuable private property near Pensacola.

I have thought it not improbable that desires the complaint made by Commanded Farrand and the Secretary of the Navy other complaints may have been made against me an account of the destruction of property and other acts I found it necessary to do.

However that may be, a few days after the date of the letter from the Secretary of the Navy to the President in regard to the burning of the unfinished gunboats General Lee relieved me from the command of the Department of Alabama and West Florida, ordered me to turn it over to my junior, and to report to General Beauregard at Corinth, where I was assigned to the command of a division, smaller it the number present for duty than the brigade I had commanded for several months in the Army of the Potomac, and by no means as well disciplined and instructed as that brigade.

I have heretofore said nothing on the subject, because the command to which I was assigned was in front of the enemy at an important point, where a general battle was daily expected. Now, hoverer, that there is no immediate prospect of a general engagement with this army, I think it proper to bring the matter to the notice of the War Department, and ask if my removal from the command of the Department of Alabama and West Florida was in any degree caused by an reports or complaints made against me by any one, or of any such complaints or report other than that made by Commander Farrand and the Secretary of the Navy have been made against me. I am convinced that it any such reports or complaints have been made I can easily show that they were without foundation, and I desire an opportunity to do so.

May I ask that you will favor me with an answer as soon as you can conveniently do so?

I am, very respectfully, your obedient servant,

SAM. JONES,

Major-General.