Police said the robbers, one armed with a suspected firearm, entered two houses at Brook Street, Omagh, at about 09:50 BST on Saturday and stole money.
One of the homes was a parochial house. No-one was injured.
Det Sgt Ian Lyle said the suspects were "aged in their 30s, with local accents and were wearing green jackets and had their faces covered".
"I would ask anyone who knows anything about this incident to contact detectives at Omagh police station on the non emergency number 101," he added.
Two priests have been robbed at gunpoint by masked men in County Tyrone.