The diplomat at the centre of the row worked at the Japanese consulate in Vladivostok
Motoki Tatsunori, its consul in the city, was freed from custody on Tuesday after being accused of espionage - and given 48 hours to leave Russia.
Moscow alleges he received secret information about its co-operation with an unnamed Asian country.
Japan denies the allegation and is demanding a formal apology.
Russia's FSB security service said it had detained Mr Tatsunori on Monday for soliciting information about "the impact of Western sanctions" on Moscow after its invasion of Ukraine in February.
"A Japanese diplomat was detained red-handed while receiving classified information, in exchange for money, about Russia's co-operation with another country in the Asia-Pacific region," the agency said in a statement.
But Japan said the detention of its consul for political affairs violated the Vienna Convention on Diplomatic Relations and had been carried out in "an intimidating manner".
"The official was blindfolded, with pressure applied to both his hands and head so he was unable to move while being detained, and then he was questioned in an overbearing way," chief cabinet secretary Hirokazu Matsuno told reporters.
He said Japan "strongly protests these unbelievable acts" and confirmed that the diplomat would leave Russia by Wednesday after being declared persona non grata.
Japan opposes the Russian invasion and is considered a hostile country by Russia - along with the US, UK and other countries which support Ukraine.
Russia and Japan also have long-standing disagreements over territory dating back to World War Two.
-- Courtesy of BBC News