Peru has announced it is withdrawing its ambassador in Tokyo due to Japan's attitude toward Peru's former leader.
Protesters have been demanding Mr Fujimori's extradition to Peru
Alberto Fujimori is in custody in Chile while Peru seeks his extradition. He has Japanese and Peruvian nationality and lived in Japan before his arrest.
Tokyo has vowed to defend the rights of Mr Fujimori and has called on the Chilean government to treat him fairly.
Mr Fujimori, 67, is wanted in Peru on charges of corruption and human rights abuses, but denies any wrongdoing.
The former president - whose parents were originally from Japan - received Japanese citizenship after fleeing Peru in 2000. Tokyo has repeatedly turned down requests from Lima for his extradition.
Peruvian Foreign Minister Oscar Maurtua met Japan's ambassador to Lima to inform him of the decision, the foreign ministry said in a statement.
"The government of Peru has decided to consider terminated the functions of the ambassador of Peru in Japan," the foreign ministry said in a statement.
"Any intervention by Tokyo in the extradition process under way with Chilean authorities for the ex-President Alberto Fujimori will constitute an unacceptable interference."
However, officials in Tokyo said they had not been officially informed of the withdrawal.
"I don't think it is related to Fujimori," Foreign Minister Taro Aso said.
Japanese diplomats had been pressing for access to Mr Fujimori following his arrest in Chile.
A delegation visited Mr Fujimori in custody on Thursday, and said that he was in good health.
A high-level Peruvian delegation is in Santiago for extradition talks. But Chile says the request will have to run its course through the courts.
Chile has also expressed concern about Japan's role in the case.
Mr Fujimori, who was president from 1990 to 2000, faces a long jail sentence if sent back to Peru.
He has vowed to run for the Peruvian presidency next April despite being barred from holding public office until 2010.