Gen. Ahmed Bakr, head of security in North Sinai, says the three were now in the protection of Egyptian security officials in Sinai.
Rev. Michel Louis, Lisa Alphonse and their Egyptian tour guide were taken hostage from a bus that was on a church trip between Cairo and Mount Sinai on Friday. Louis is the pastor of a Pentecostal church in Boston.
The kidnapper, Jirmy Abu-Masuh, says he freed them after officials promised they would work on releasing his uncle from prison. Abu-Masuh says his uncle was only placed there because he refused to pay a bribe to police, but Egyptian security officials said the uncle was ordered to a 15-day prison sentence for drug possession.
Family members and parishioners prayed for their release this weekend.
"The only concern that we have at the moment is that he is diabetic, and the longer they hold him, I assume that it's not going to work in his favor," said Louis's son, Jean.
The Associated Press contributed to this report.