The move came after detainees covered surveillance cameras and windows, a US Army spokesman said.
He said some prisoners used "improvised weapons" and in response "four less-than-lethal rounds" were fired.
The Pentagon says 43 prisoners are on hunger strike, but lawyers for the detainees say the number is higher.
Almost a dozen are being force-fed, according to military officials.
There were no "serious injuries to guards or detainees" in Saturday's clashes, according to Capt Robert Durand of the US military's Southern Command.
"I know for sure that one detainee was hit but the injuries were minor, just some bruises," another spokesman, Col Greg Julian, told the Associated Press.
Lawyers for some of the detainees condemned the camp authorities' actions.
Carlos Warner, who represents several detainees, told AP that "the military is escalating the conflict". Detainees' frustration
Hunger strikes have happened frequently at the US military prison, but this protest, which began in February, is reportedly one of the longest and most widespread.
However, Guantanamo officials deny claims that the strike began after copies of the Koran were mishandled during searches of prisoners' cells.
Human rights groups and lawyers representing the prisoners say it reflects growing frustration at the US military's failure to decide the detainees' future.
Nearly 100 of the detainees have been reportedly cleared for release but remain at the facility because of Congressional restrictions and also concerns of possible mistreatment if they are sent back to their home countries.
The military detention centre opened in 2002 to hold suspects captured in counter-terrorism operations after the 11 September 2001 attacks in the US.