Brigadier-General Janis Karpinski told officials investigating prisoner abuse at Abu Ghraib that the child was crying and wanted to see his mother.
Karpinski's statement is among hundreds of pages of US army records about Abu Ghraib the American Civil Liberties Union (ACLU) released on Thursday.
The ACLU got the documents under a Freedom of Information Act lawsuit seeking records about abuse of detainees in Iraq.
Karpinski did not say what happened to the boy in her interview with Major-General George Fay. Military officials have previously acknowledged that some juvenile prisoners had been held at Abu Ghraib, a massive prison built by Saddam Hussein's government outside Baghdad.
On another subject, Karpinski said she had seen written orders to hold a prisoner that the CIA had captured without keeping records. The records also quote an unnamed army officer at Abu Ghraib as saying military intelligence officers and the CIA worked out a written agreement on how to handle unreported detainees, known as "ghosts".
A US army report issued last September said investigators could not find any copies of any such written agreements.
Karpinski (L) was the prison
commander at Abu Ghraib
The Pentagon has acknowledged holding up to 100 "ghost detainees", keeping the prisoners off the books and away from humanitarian investigators from the International Committee of the Red Cross.
Defence Secretary Donald Rumsfeld has defended the practice, saying he authorised it because the prisoners were enemy combatants not entitled to prisoner of war protections.
The ACLU sued Rumsfeld earlier this month on behalf of four Iraqis and four Afghans who say they were tortured at US military facilities. Rumsfeld and his spokesmen have repeatedly said he and his aides never authorised or condoned any abuses.
Six enlisted soldiers have pleaded guilty to military charges for their roles in abuses at Abu Ghraib, and Private Charles Graner Jr was convicted at a court martial earlier this year and sentenced to 10 years in prison.
Karpinski, one of the few generals to be criticised in army detainee reports for poor leadership, quoted several senior generals in Iraq as making callous statements about prisoners.
Karpinski said Major-General Walter Wodjakowski, then the second highest ranking army general in Iraq, told her in the summer of 2003 not to release more prisoners, even if they were innocent.
"I don't care if we're holding 15,000 innocent civilians. We're winning the war," Karpinski said Wodjakowski told her.