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The provision of the Constitution dealing with habeas corpus is found in Article I, dealing with the legislative power vested in Congress, and provides that the writ of habeas corpus shall not be suspended unless in time of war or rebellion the public safety shall require it. The question of whether only Congress may suspend it has never been authoritatively answered to this day, but the Lincoln Administration proceeded to arrest and detain persons suspected of disloyal activities.
Originally posted by Bleys
The article states that Chief Justice Roger Taney attempted to order Lincoln to show just cause for suspending the writ of habeas corpus but was basically ignored. Taney went on to issue a court opinion the stated that only the Congress had authority to suspend the writ of habeas corpus not the President. This also went ignored by Lincoln.
Without the sanction of law the federal government arrested men by the thousands and confined them in military prisons. The number of such executive arrests was certainly over 13,000, and it has been estimated to have been as high as 38,000 (Columbia Law Review, XXI, 527–28, 1921). This policy was bitterly criticized in some quarters, but it is generally assumed that the people as a whole supported the arrest policy.