The ruling on Monday, which is certain to dismay human rights activists worldwide, also allows the administration to keep away from the public domain other basic details of the detainees and those questioned.
Without comment, the top court refused to hear an appeal by civil liberties and other groups which are challenging the secret arrests and detentions on the grounds that they violate the Freedom of Information Act and constitutional free-speech rights under the First Amendment.
The justices let stand a US appeals court ruling that disclosing the names could harm national security and help "al-Qaida in plotting future terrorist attacks or intimidating witnesses in the present investigation."
Although the high court stayed out of the dispute involving the names of those detained, it has agreed to hear other cases arising from the Bush administration's war on terror.
Those cases involve the president's power to detain American citizens captured abroad and declared "enemy combatants" and whether foreign nationals can use American courts to challenge their incarceration at the US military base in Guantanamo Bay in Cuba.
US highhandedness in dealing with "terror suspects" has been a subject of global consternation in recent times.
It has been holding without charge 660 suspects, mostly foreign nationals, in Guantanamo Bay since the Afghanistan war. Most are faced with bleak prospects of an early trial even two years after their detention.
Human rights groups have condemned the continuing detentions and alleged the detainees have been sucked into a "legal black hole".