Merah died in a police assault on his flat in Toulouse on Thursday after a 32-hour siege.
The Paris Normandie newspaper says students walked out after the teacher in Rouen called Merah “a victim”.
The Minister for State education, Luc Chatel (pictured), asked the vice-chancellor of Rouen to immediately suspend this teaching.
The teacher is also reported to have said Merah’s links to al-Qaeda were invented by the media and French President Nicolas Sarkozy.
Mohamed Merah died in a shoot-out at his flat in Toulouse on Thursday
The local head of the SGEN-CFDT trade union, Pascal Bossuyt, said that the woman “said something unfortunate in a particular context and she immediately regretted what she said”.
Merah shot dead three Jewish children and a rabbi as they arrived at school on Monday morning, and he killed three soldiers a few days before.
French schools had held a minute’s silence for the victims of the shootings after the attack on the Jewish site
Most of the students walked out of the Rouen classroom although a few remained, saying they were trying to understand what the teacher was talking about, Paris Normandie said.