Alex Bargmann, Studied U.S. History in Undergrad
Yes. On a few clear occasions and at times, with somewhat blurrier lines.
During Reconstruction, after the Civil War as the federal government attempted to rebuild the South and reunite the South and North, Congress passed an act allowing the President to suspend Habeas Corpus in cases of conspiracy against federal authority. President Grant suspended Habeas Corpus in South Carolina in 1971.
The U.S. Governor-General of the Philippines suspended Habeas Corpus in the colony in January of 1905 in response to growing unrest and requests by the local commission for suspension.
While not suspended at large federally, Hawaii suspended Habeas Corpus after the attack on Pearl Harbor. 8 German saboteurs were also tried without the application of Habeas Corpus. The U.S. Supreme Court ruled it did not apply in this case.
After the September 11th attacks, there have been several incidents, executive orders, and laws where the writ was either limited, ignored, or modified. Immediately following the attacks, in November, 2001, the President was given the ability to detain a non-citizen considered to be involved in terrorist activity without a charge, legal counsel, or court date - possibly in violation of Habeas Corpus. A 2004 Supreme Court case held up the writ and its principles for all American Citizens (Hamdi v. Rumsfeld). In 2006, Congress passed a law, Military Commissions Act, that suspended the principle for non-citizen combatants. Later, the Supreme Court ruled the law unconstitutional - litigation around the law continues after the Dept. of Justice claimed the law was not unconstitutional. The court ruled again that it was. Since then, Obama has issued an order that the detainees at Guantanamo have a constitutional right to the Write of Habeas Corpus.