It is not yet clear whether Mugabe will be deposed but the main goal of the generals appears to be stopping his wife Grace from succeeding him.
Grace was being lined up to succeed her 93-year-old husband after her rival, vice president Emmerson Mnangagwa, was fired just over a week ago.
There are conflicting reports over the current location of the First Lady who is known for her lavish spending and increasing political influence.
The Zimbabwean army said it took Mugabe and his wife into custody during the coup which it described as a “bloodless transition”.
But according to Sky News sources, Mrs Mugabe has fled across the border to Namibia.
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Nick Mangwana, a Zanu-PF representative in the UK, told BBC that he had received reports that First Lady Grace Mugabe is no longer in the country.
Opposition MP Eddie Cross told BBC News that he believes Grace had fled to Namibia and understands that she was allowed to leave the country last night by the army.
Nevertheless there now suggestions that Grace is not in Namibia fafter all.
According to Namibian newspaper New Era, Namibia’s International Relations Minister Netumbo Nandi-Ndaitwah has dismissed reports of Grace having fled to Namibia.
Zimbabwean newspaper publisher Trevor Ncube has suggested that Grace actually remains with her husband in Zimbabwe.
He tweeted: “My sources in Zimbabwe confirm Grace Mugabe is still at the ‘Blue Roof’ home in Borrowadale, Harare with President Mugabe.”
Grace was the president’s secretary and mistress until 1996 when his wife died, and they married in a lavish public ceremony.
The First Lady was widely believed to be lining herself up to step into her husband’s shoes upon his death and trying to build support among members of Zanu-PF.
Grace Mugabe is nicknamed ‘Gucci Grace’ by her critics and is known for her lavish spending on luxury items, making her deeply unpopular with many ordinary Zimbabweans.