In a speech to students, he praised the example of India and Pakistan, where he said partition saved many lives.
Splitting Nigeria "would stop the bloodshed and burning of places of worship," state news agency Jana quoted him as saying.
A senior Nigerian diplomat said he was not taking the suggestion seriously.
Hundreds of people have died in communal violence in villages around the central Nigerian city of Jos this year.
The BBC's Rana Jawad in Tripoli says Col Gaddafi's suggestion is unsurprising given his past form.
Last year, he called for Switzerland to be abolished and for its land to be divided between Italy, Germany and France.
'Historic, radical solution'
Although the violence in Nigeria generally takes place between Muslim and Christian communities, the underlying causes are a complex mix of political, social and economic grievances.
Nigeria is roughly split between its largely Muslim north, and a Christian-dominated south.
Col Gaddafi, until recently head of the African Union, characterised the Jos violence as a "deep conflict of religious nature" caused by the federal state, "which was made and imposed by the British in spite of the people's resistance to it".
He described the partition of India as a "historic, radical solution" which saved the lives of "millions of Hindus and Muslims".
Splitting India in 1947 caused a breakdown of law and order in which at least 200,000 people died. Some estimates say one million people were killed.
About 12 million people were left homeless and thousands were raped.
An attempt by the Igbo people of south-eastern Nigeria to secede in 1967 sparked a war which left more than one million people dead.
Source: BBC
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