The priest, Fidelis Mukonori, is acting as a middleman between Mugabe and the generals, who seized power on Wednesday in a targeted operation against "criminals" in his entourage, a senior political source said.
The source could not provide details of the talks, which appear to be aimed at a smooth and bloodless transition after the departure of Mugabe, who has led Zimbabwe since independence in 1980.
Mugabe, still seen by many Africans as a liberation hero, is reviled in the West as a despot whose disastrous handling of the economy and willingness to resort to violence to maintain power destroyed one of Africa's most promising states.
Zimbabwean intelligence reports suggest that former security chief Emmerson Mnangagwa, who was ousted as vice president this month, has been mapping out a post-Mugabe vision with the military and opposition for more than a year.
Fueling speculation that that plan might be rolling into action, opposition leader Morgan Tsvangirai, who has been receiving cancer treatment in Britain and South Africa, returned to Harare late on Wednesday.