The two emails, released to The New York Times by Hasan's civilian lawyer, expressed concern about what he learned from soldiers he was evaluating as a military psychiatrist.
Hasan asked his supervisors and Army legal advisers how to handle three cases that disturbed him.
One of the cases dealt with a soldier who said American troops had poured 50 gallons of fuel into the Iraqi water supply as revenge.
Another case involved a soldier who told Hasan about the mercy killing of a severely injured insurgent while a third case involved a soldier who said he killed an Iraqi woman because he was told to shoot anything that approached a specific site.
"I think I need a lot of reassurance for the first few times I come across these," Hasan wrote. Below his email signature, he included a quote from the Koran that read: "All praises and thanks go to Allah, the cherisher and sustainer of all the world."
Hasan's radical beliefs and his correspondence with his Army superiors have played a limited role in his court-martial, now in its third week at Fort Hood.
Prosecutors wanted to use several pieces of evidence that showed his ideology, including emails he exchanged with an American-born cleric in Yemen but the presiding judge Monday prohibited them from being presented to the jury.
Hasan is charged with 13 counts of premeditated murder and 32 counts of attempted murder for a shooting rampage at the base in November 2009.