The question came after a speech Bush made at a Faith and Freedom Coalition summit in Washington.
"I don't know what was on the mind or the heart of the man who committed these atrocious crimes," Bush said in his remarks. "But I do know what was in the heart of the victims."
Soon after reporters noted the line, Bush spokesman Tim Miller said on Twitter that "of course" the former governor thought the attack was racially motivated.
In his speech, Bush went on to meditate on the fact that the massacre -- which resulted in the deaths of nine African-Americans including South Carolina state Sen. Clementa Pinckney (D), pastor at the Emanuel African Methodist Episcopal Church -- took place in a house of worship.
"They were praying. They were learning and studying the word of the Lord," Bush said. "In times like these, in times of great of national mourning, people of faith, all of us must come together and at least reflect on this and fortify our strength and love of Christ, love of God to be able to continue to go forth."
Bush said the shooting had a "big impact" on him, and urged his audience to "support" each other and to “continue to bear witness to the truths that God acts through us.”
"Even in crisis, even in desperate times, we can always walk upright as brothers and sisters and look to the heavens and know that we’re Children of God," Bush said. "I know your hearts and prayers are with the families and the pastor who lost their lives and let’s hope it never ever ever happens again."
Bush had a campaign event planned in Charleston Thursday, which he canceled in light of the shooting.
This story has been updated with additional comments by Bush and his spokesman.