Top Iraqi commander Lt Gen Abboud Gambar unveiled the plan, which will include a longer curfew for the city, live on television.
The US-backed security drive is also now being debated in the US Congress.
BBC correspondents say closing borders will be difficult as they are long, porous and often barely guarded.
Sweeping powers
Thousands of extra US troops are heading to the Iraqi capital to bolster Iraqi forces in the new security "surge" against militants and bombers.
US President George W Bush is committed to sending 21,500 additional troops to Iraq, but he faces strong opposition in the Democrat-led Congress.
Gen Gambar, speaking on behalf of the Cabinet and Prime Minister Nouri Maliki, did not say when the borders would close.
Officials told the BBC the curfew in Baghdad would be extended by one hour, starting at 2000 local time (1700 GMT) instead of 2100, and continuing to 0600.
Officials also said that after the 72-hour border closure, the frontier with Iran would only be partially reopened.
Gen Gambar is in charge of a plan that will divide Baghdad into 10 security districts in an attempt to drive out insurgents and illegal militias.
He said the plan would give him sweeping new emergency powers, combining the command of the police and armed forces.
Weapons permits would be restricted to the Iraqi and US military.
The BBC's Andrew North in Baghdad says the Iraqis want to be seen taking the lead on the security drive but there were few specifics and a lot of questions have been left unanswered.
The border move comes amid claims by the US that Iran is supplying militias with sophisticated weapons to attack US troops. Tehran rejects the accusation.
Violence continued in Iraq on Tuesday despite the new security plans.
A van crammed with explosives detonated near a college in western Baghdad, killing at least 16 people and injuring 45.
The attack is the latest in a string of deadly incidents in Baghdad.
On Monday a series of car bombs in markets in the centre of the capital killed at least 76 people and wounded 164.