His intervention last week followed protest from historians, teachers and human rights and anti-racism groups who object to the glorification of the empire - which they say caused exploitation and suffering - and to the imposition of a politicised "official history".
Laws were passed last February recognising the part played by French colonialists repatriated from Algeria, and by Algerians who fought with the French in the bloody war of independence (1954-1962).
A contentious clause was added by MPs from President Chirac's ruling conservative UMP party sympathetic to former French settlers in Algeria. It says school lessons must recognise "the positive role of the French presence overseas, notably in north Africa", and acknowledge the "distinguished position" due to the "history and sacrifices of combatants of the French army who came from these territories".
A petition against the clause last year said "retaining only the 'positive role' of colonialism imposes an official lie about crimes, about massacres sometimes going as far as genocide, about slavery, about racism inherited from this past".
The row has echoes in the UK, where Chancellor Gordon Brown has said Britain should stop apologising for its colonial past, while Labour MP Gordon Marden, a former editor of History Today and member of the education select committee, has called on schools to teach a rounded history of the rise and fall of Britain's empire.
Professor Claude Liauzu, who launched the petition, told The TES that since 1870 history teachers in France had had total freedom to teach within the framework of the ministry's curriculum.
"The reason for our refusal (to accept this law) is defence of freedom of teaching, which goes beyond the colonial problem," he said.
Hubert Tison, general secretary of the Association of History and Geography Teachers, which wants the clause withdrawn, said there was no place for "official history".
A history teacher at a Paris secondary school said teachers were considering a boycott if ordered to abide by the clause.
After an unsuccessful opposition attempt to repeal the clause in November, protests included a petition of 44,000 signatures. In response, President Chirac commissioned Jean-Louis-Debre, president of the national assembly, "to assess the action of parliament in the domain of history and memory".
Last week, Mr Chirac said the present law was dividing the French people, and "it must therefore be rewritten". He promised that Mr Debre's new version would restore calm.