Kamal al-Jarrah, the ministry's director of public relations and cultural affairs officer, was gunned down in front of his home in the west of the capital as he left for work, said a ministry official on Sunday.
It was the second assassination of an interim government official in as many days.
The unidentified armed men killed Jarrah, 63, in the Ghazalia neighbourhood of Baghdad. He died of his wounds at Yarmuk Hospital.
Al-Jarrah was primarily responsible for dealing with exchange programmes and relations with foreign countries and UNESCO. He had worked in the education field for 40 years, said ministry official Abd al-Khaliq al-Amri.
The assassination comes a day after another senior Iraqi official, deputy foreign minister Bassam Kuba, was killed by unknown assailants in Baghdad.
With the 30 June transfer of power nearing, unrest continues to grip Iraq.
Musa Jabar was injured in a car
bombing in southeast Baghdad
Sixteen Iraqis, including four policemen, were killed in a car-bomb explosion outside a military training academy on Sunday, reported Aljazeera's correspondent.
Two Iraqi police convoys were patrolling the Rustumiya area in southeast Baghdad when a parked car exploded, reported correspondent Abd al-Adhim Muhammad.
A number of civilians were killed and many others injured.
Also, two Iraqis working for US-funded Iraqi television network al-Iraqiya were found dead near the Syrian border, colleagues said on Sunday.
They said television technician Abd al-Karim al-Haidary and driver Jawad Qazim were killed on Saturday. The motive was
Meanwhile, in the restive town of Baquba, the director of police survived an assassination attempt, reported our correspondent.
Brigadier General Majid al-Mani came under gunfire by unidentified assailants in the town northeast of the capital.
Also on Sunday, one US occupation soldier was killed and two
wounded in a roadside bomb and small arms attack near Taji, 20km north of Baghdad, a US military spokesperson said.
"One US soldier was killed and two wounded by an improvised
Senior diplomat Bassam Kuba
was assassinated on Saturday
explosive device and small-arms fire attack at 12:30 pm. The unit returned fire, killing one attacker," the spokesperson said.
Earlier, an explosion rocked the US occupying administration's headquarters in Baghdad. Military officials said they believed the blast at the heavily fortified Green Zone was a rocket attack.
Sirens had sounded after the blast to warn staff to take
cover, as a plume of smoke rose from the compound on the west bank of the Tigris river.
The Green Zone often comes under mortar and rocket attack
from resistance fighters opposed to the US-led occupation.
Elsewhere, another six Iraqis were killed in clashes overnight between US occupation troops and fighters loyal to Shia leader Muqtada al-Sadr in a Baghdad suburb.
The fighting in the al-Sadr City suburb claimed the lives of two Mahdi Army fighters, said medical sources and family members. Another four victims were identified as civilians.