The incidents allegedly took place in May at Camp Bucca, a vast desert camp where the US military houses 18,000 of its 21,000 prisoners in Iraq.
The six sailors were charged with assault on detainees and will face courts-martial at Camp Bucca within the next 30 days, the navy said.
"The day that this all took place there had actually been some unrest at the camp. There had been some detainee-on-guard issues, which ranged from spitting to throwing bodily functions at some guards," Campbell said.
The use of pepper spray in warfare is banned by international treaties on chemical weapons, but many governments say their armed forces are permitted to use it in conflict zones for law-enforcement duties.
Seven other sailors received non-judicial punishment for failing to report the incidents, Campbell said.
Two had their charges dismissed while others were reduced in rank or faced suspended punishment, she added, declining to be more specific.