The state-run Zimbabwe Herald newspaper published what it called new photos of the meeting, saying details were to come.
One showed Mugabe and the army commander shaking hands.
The photos did not show first lady Grace Mugabe, whose rapid political rise had alarmed many in the country who feared she could succeed her husband.
Seizing on the political limbo to speak out, civil society groups and opposition leaders urged Mugabe to step aside after 37 years in power and for the country to transition into free and fair elections.
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Mugabe has been in military custody, reportedly with his wife, since the army stepped in overnight Tuesday. There was no sign of former Vice President Emmerson Mnangagwa, whose firing last week angered supporters in the military amid concern that Grace Mugabe would take his place at a party meeting next month.
A joint statement by more than 100 civil society groups urged the 93-year-old Mugabe, the world's oldest head of state, to peacefully step aside and asked the military to respect the constitution. A joint statement by churches also appealed for calm.
One analyst said he believed the negotiations "have pretty much reached an end point" to get Mugabe to step aside and that it was a "matter of hours or days."
Knox Chitiyo, associate fellow with the Africa program at Chatham House, warned that speculation remains high but said the aim was a peaceful, managed transition. He said the military wants a dignified exit for Mugabe, who has ruled since independence from white minority rule in 1980 and remains widely known, even praised, in Africa as a liberation leader.
Opposition leaders spoke out but said they had not been contacted as part of the Mugabe negotiations.
Opposition leader Morgan Tsvangirai, who shared power with Mugabe between 2009 and 2013, said Mugabe must resign and said his party would participate in talks on a transitional mechanism if approached.
He pointedly referred to Mugabe as "Mister."
A vice president who was fired in 2014, Joice Mujuru, called for "free, fair and credible elections" following a transition arrangement that draws from a range of communities.
Across the country, Zimbabweans long frustrated by crackdowns on dissent and a collapsing economy were enjoying freedoms they haven't had in years. For once, they weren't contending with bribe-seeking police officers who mounted roadblocks every few miles (kilometers).
Soldiers manning the few checkpoints leading into downtown Harare greeted motorists with a smile, searching cars without hostilities and wishing motorists a safe journey.
"The situation is quite OK because they are now returning to their jobs," said one resident, Clinton Mandioper.
Human rights groups urged respect for rights as the drama played out.
Amid questions about the whereabouts of first lady Grace Mugabe, one Namibian newspaper, the New Era, reported that the country's foreign minister denied she had fled there.
The US Embassy advised citizens in Zimbabwe to "limit unnecessary movements" as political uncertainty continues. The British government also urged its citizens to avoid large gatherings and any demonstrations.