Mugabe's decades-long grip on power appeared to be fading as military vehicles blocked roads outside the parliament in Harare and senior soldiers delivered a late-night television address to the nation.
"The president and his family are safe and sound and their security is guaranteed," Major General Sibusiso Moyo said, slowly reading out a statement.
"We are only targeting criminals around him who are committing crimes... As soon as we have accomplished our mission we expect that the situation will return to normalcy."
Moyo said: "This is not a military takeover of government".
But the generals' actions posed a major challenge to the 93-year-old Mugabe, who has ruled Zimbabwe since independence from Britain in 1980.
Neighbouring South Africa's President Jacob Zuma, one of Mugabe's closest allies, said he had spoken to the veteran leader by telephone.
Mugabe "indicated that he was confined to his home but said that he was fine," the South African government said in a statement that called for calm and restraint.
Tensions between Mugabe and the military establishment, which has long helped prop up his authoritarian rule, erupted in public over recent weeks.