Senate Republican leader Mitch McConnell said bringing the suspects from Guantanamo into the US was would put "Americans unnecessarily at risk".
The five will be tried in a civilian court near Ground Zero. The prosecution says it will seek the death penalty.
Democrats hailed the decision, while families of 9/11 victims are divided.
The move is part of US President Barack Obama's efforts to close the Guantanamo detention centre for terror suspects.
We have a president who doesn't know we're at war
Debra Burlingame
9/11 relative
In quotes: US 9/11 trial reactions
New York voices on 9/11 trial
A triumph of justice?
"The Department of Justice will pursue prosecution in federal court of the five individuals accused of conspiring to commit the 9/11 attacks," US Attorney General Eric Holder told a news conference.
"I fully expect to direct prosecutors to seek the death penalty against each of the alleged 9/11 conspirators."
But Republican leaders immediately criticised the move.
Senate Republican leader Mitch McConnell said described it as "a step backwards for the security of our country" that "puts Americans unnecessarily at risk".
