Police said Zobaa Yassin was shot dead on Sunday in his car along with his driver. Yassin was one of the leading civil servants in the ministry.
Groups battling Iraq's US-backed government have assassinated dozens of government officials. Last year, in the most high-profile assassination, the head of the now-defunct Iraqi governing council was killed by a car bomb.
Since Jaafari announced his partial line-up on 28 April, fighters have stepped up their attacks, leaving some 150 people dead, mostly civilians.
Fifteen people - two civilians, an Iraqi soldier and 12 fighters -were also killed in a huge gunbattle that broke out after a US checkpoint was attacked on Tuesday in the western stronghold of Ramadi.
The military also announced the death of a soldier in a bomb attack near Baghdad airport on Monday, as the death toll from a week of bloodshed mounted.
Meanwhile, AFP reported the deaths of two Iraqi soldiers and the wounding of four civilians - including one child - after a car bomb exploded at a military checkpoint in north Baghdad. US soldiers were also seen removing the burnt out wreck of a humvee.
A senior water ministry official was gunned down in southern Baghdad in broad daylight last week, whilst three policemen were killed in separate attacks north of the capital, security sources said.
And a car bomb exploded in the northern city of Mosul killing one civilian, and further south, an Iraqi soldier and a businessman working for the US military were gunned down on Friday.