Air Marshal Shiri is the first senior figure to be targeted for many years
The commander of Zimbabwe's air force has been wounded in what officials are calling an assassination attempt.
Perence Shiri, 53, a close ally of President Mugabe, seen as one of the most feared military leaders, was shot in the arm and is said to be stable.
The opposition MDC says he was one of the masterminds of violence against its supporters during this year's election.
Its spokesman said the attack was aimed at justifying a military crackdown and eventual declaration of an emergency.
The incident comes as pressure grows on Zimbabwe to allow international mediation in its political crisis.
The crisis is compounded by a cholera epidemic which has left hundreds dead.
On Monday, at the UN Security Council's first discussions on Zimbabwe since July, Secretary General Ban Ki-Moon said the world was witnessing a failure of the leadership in Zimbabwe to address the crisis.
After disputed presidential elections in March, President Robert Mugabe's Zanu-PF party and the opposition Movement for Democratic Change (MDC) agreed to form a power-sharing government.
But implementation of that agreement, reached in September, has been dogged by disagreements over whose supporters would get key ministries.
Correspondents say this is the first time such a senior government figure has been the target of a violent attack for many years.
Accused of masterminding attacks on opposition in 2008
Member of Joint Operations Command - top military body
Accused of leading farm invasions in 2000
Led brutal campaign against "dissidents" in 1980s, which left 20,000 dead
Called himself "Black Jesus" - as he had the power of life or death
Cousin of Robert Mugabe
On sanctions list of US, EU
"This is a very, very unusual incident, because Zimbabwe does not have a history of assassinations," the assistant editor of the state-run Herald newspaper, Caesar Zaye, told the BBC World Service's World Today programme.
Air Marshal Shiri was ambushed on Saturday evening while driving to his farm, state media said.
Police said he was accosted by unknown people who shot at his car.
When he heard the gunshots, he got out thinking it was a puncture and was shot. He is now said to be recovering in hospital.
Officials said the incident was one of a series of attacks aimed at destabilising the country.
"The attack on Air Marshal Shiri appears to be a build-up of terror attacks targeting high-profile persons, government officials, government establishments and public transportation systems," the Chronicle newspaper quoted Home Affairs Minister Kembo Mohadi as saying.
There were several bomb blasts around Harare last year which caused little damage. The courts have acquitted several opposition activists accused of staging the attacks.
Mr Zaye said the alleged assassination attempt was "an attempt to bring a security angle into the crisis".
However, other sources suggest the cause was either a feud within the ruling Zanu-PF party or an attempted robbery.
On Monday, Zimbabwe's government said it had "compelling evidence" that neighbouring Botswana was hosting military training camps for opposition groups intent on bringing about regime change.
Botswana denied the charges, and said Harare had failed to provide any tangible evidence to back up its allegations.
Air Marshal Shiri, who is also Mr Mugabe's cousin and a loyal supporter since he came to power, sits on the Joint Operations Command which advises the president on military matters.
The opposition Movement for Democratic Change said the JOC was behind the violent attacks on its supporters ahead of June's presidential run-off - allegations the military strongly denied.
Air Marshal Shiri was commander of the Fifth Brigade, blamed for the killing of 20,000 people in Zimbabwe's south-western Matabeleland region during the 1980s.