The explosion occurred at around 4:30 am (0330 GMT) near the home in Nantes, western France, of Aissa Dermouche, police sources said.
On Wednesday, Dermouche, who is a Muslim, was appointed prefect of the eastern Jura area, a post which gives him regional responsibility for law and order.
"There is no doubt that this concerns a criminal act," Jean- Marie Huet, state prosecutor in Nantes, said of the explosion. Police sources said the car was empty at the time of the blast and no one was hurt.
Dermouche's Jura appointment fuelled a debate about the integration of minorities before regional elections in March, when the far-right National Front aims to cash in on racial tensions.
President Jacques Chirac, who insisted on Wednesday that Dermouche's appointment was based on merit, was outraged at the explosion.
"This attack targeted the new prefect personally and the symbol that he represents"
Jean- Marie Huet,
State prosecutor in Nantes
"(The president) asks that the perpetrators of this very serious act be pursued and severely punished," Chirac's office said in a statement.
Huet said the attack was well prepared. "This attack targeted the new prefect personally and the symbol that he represents," he said. "Tests have been carried out on the shell of the vehicle so we can conduct analyses to determine the nature of the explosive used."
Dermouche, 57, was not the first member of a minority to be
nominated for an influential post in France, but his appointment was particularly sensitive at a time when the country is debating how to better integrate its Muslim minority.
The attack underlines the problems in assimilating France's five million Muslims and other minorities. On Saturday, thousands of Muslims protested against a looming ban on Muslim headscarves in French state schools.
Many French politicians and voters support the planned law as a bulwark against Islamist influence among Muslim immigrants.
The centre-right government hopes the headscarf ban will prevent the National Front from cashing in on racial strife in the March regional elections. Many on the far right resent immigrants taking influential posts.
"Symbols of the Republic and the authority of the state cannot be attacked"
Dermouche symbolises success among France's immigrants. Born in an Algerian village, he later came to France and had been director of the Ecole Superieure de Commerce business school in Nantes since 1989, before being appointed prefect of Jura.
Although his appointment was surrounded by talk about positive discrimination, officials insisted he was qualified.
Justice Minister Dominique Perben, speaking in Strasbourg, told reporters that security around Dermouche would be stepped up: "Symbols of the Republic and the authority of the state cannot be attacked," he said.