A plume of smoke could be seen rising from the area near the hospital after the attack on Tuesday and helicopters circled overhead.
Sirens sounded the alarm and loudspeakers could be heard issuing instructions to personnel in the area.
Security inside the zone was boosted this month after reports that bombers were trying to penetrate the area, which is a frequent target for attacks.
Police said at least two other rounds exploded in downtown Baghdad.
Tal Afar offensive
Meanwhile, US commanders in Tal Afar said that more than 400 suspected fighters were in custody as a result of the offensive there.
The Iraqi military reported on Tuesday that its troops had detained 36 more fighters, including a Yemeni citizen, just south of Tal Afar.
The Tal Afar offensive has been
criticised by the city's leaders
"This operation was very precise. We've had access to all the terrorist safe havens," said Brigadier-General Muhsen Yahya, commander of the Iraqi Army's 1st Brigade in Tal Afar.
Aljazeera has learned that an al-Qaida official in Tal Afar, Hasan Muhammad Ali, also known as Abu al-Qasim, and two of his guards, had been killed in an air strike on the city.
On Monday, officials said the toll in three days of fighting in Tal Afar totalled 200 fighters.
Seven Iraqi soldiers and six civilians also died, while the US military said no American soldiers were hurt.
Prime Minister Ibrahim al-Jaafari flew to Tal Afar on Monday to congratulate his army, and Al-Iraqiya state television said he went despite fighters threats "to attack the city with chemical and biological weapons".
An Iraqi journalist in Tal Afar, Nasir Ali, told Aljazeera that a group of the city's prominent Sunni figures and religious leaders met al-Jaafari.
They believe his government did not fulfil promises made to the city's leaders during a meeting which took place a day before the raid on the city.
Ibrahim al-Jaafari has visited Tal
Afar to congratulate his army
Tal Afar's prominent residents also condemned the behaviour of Iraqi police commandos who were sent from Baghdad and caused much damage to the city, Ali said.
The commandos looted and burnt down the homes of those who fled the city, Ali added.
These commandos also randomly arrested young and old Sunni Iraqis. Tribal leaders and religious scholars were among those detained.
The police officers also arrested displaced Iraqis who were staying in tents, reported the journalist.
There was no known public threat from fighters to use unconventional weapons in Tal Afar, but armed groups made two internet postings in recent days vowing to stage chemical attacks on the Green Zone.
The Islamic Army in Iraq, which has previously claimed responsibility for abductions and killings of foreigners, made the bounty offer for the assassination of key Iraqi officials.
The group called in a web posting for its "fighters to strike the infidels with an iron fist".
It offered $100,000 to the killer of al-Jaafari, $50,000 for Jabr and $30,000 for al-Dulaimi.
In other developments on Tuesday:
- Armed men shot and killed two Sunni clerics in Baquba, a town 60km northeast of Baghdad.
- Two truck drivers delivering concrete blast walls from a factory in Iraqi Kurdistan were ambushed and killed in Baghdad's Dora neighbourhood. The blast walls are used throughout Baghdad to secure government buildings, hotels, embassies and other potential targets from bombers.
- Police found the body of a former judge in Baghdad's eastern neighbourhood of Sadr City. A note left next to it said: "This is the destiny of those who support Saddam."
- A bomb planted on board a minibus exploded in Hilla, a town 95km south of Baghdad. Two civilians were killed and 6 injured, police said.
- In Samarra, north of Baghdad, US soldiers killed two attackers who were trying to plant a roadside bomb, the military said.
Also on Tuesday, state-run Anatolian news agency said three Turkish engineers captured by fighters in Iraq two months ago were released and returned to Turkey,
The three men were shown on a video released to Arabic television last month in which their captors said they were issuing a "last warning" to companies dealing with US-led forces in Iraq.
Truckers are often attacked or
captured by armed groups
"They didn't push us around at all, but every night they threatened to kill us, saying, 'We will cut off your heads'," the agency quoted one of the men, Fatih Yigit, as saying after reaching the Turkish border.
"The only thing our captors wanted was for our firm to pull out of Iraq," he said.
The three men were released near the central city of Beiji on Monday morning, the agency said, but it was not immediately clear whether their company had stopped its Iraq operations.
"My life has been saved," said Yigit. "I don't want any Turkish citizen to risk his life there - no Turk should go to the Arab part of Iraq."
More than 200 foreigners have been captured since the 2003 US invasion of Iraq.
Some have been released - often after payment of ransoms - but some have been killed. Many more Iraqis have been kidnapped, usually for ransom.