The plant in the northern region of Aomori is expected to begin operations next month, but critics charge that it poses an environmental safety risk and could also be vulnerable to an earthquake.
Undaunted, Fillon said Paris and Tokyo, which are major nuclear supporters, should seek to vaunt the benefits of sharing that technology with developing nations too.
"It is important France and Japan are the spokesnations of the reasonable use of nuclear on a global scale," he told reporters.
He said refusing emerging economies access to civil nuclear rights would be "a political mistake."
"Step by step, by respecting all the security rules, we would like to bring developing nations toward mastery of these technologies," he added. "It is a very important political trend."
Fillon said he hoped Paris and Tokyo would be able to press for a "common action in favour of civilian nuclear energy" at a July summit of the G8 group of the world's leading industrialised nations, which Japan is hosting.
Some 700 protesters rallied in Aomori, the main town in the prefecture of the same name and near Rokkasho, where the facility was built by Japan Nuclear Fuel (JNFL) and France's nuclear giant Areva.
The nuclear reprocessing plant is "the biggest and most dangerous obstacle to directing Japan towards a safe and clean energy future," the environmental group Greenpeace said in a statement.
"Areva is aggressively promoting nuclear power expansion despite the risks, poor value for money and ineffectiveness in combating problems such as climate change," it added.
Protesters also worried about a possibly active quake faultline.
A major quake could trigger "an enormous amount of radiation leakage (that) will affect not only local residents here, but also the global environment," said Koji Asaishi, a lawyer involved in four lawsuits focused on the possible existence of an active faultline.
A map published by Japan's Active Fault Research Center does not specify a faultline in Rokkasho, but shows at least seven in Aomori Prefecture.