Nahid and Shahriar - both employees at a private bank -- were arrested from Rajshahi city, about 150 kilometres south northern district of Rangpur where Hoshi Kunio was shot dead, the DailyStar reported.
A joint team of Detective Branch of Police and Police Bureau of Investigation from Rangpur carried out the arrests, said Humayun Kabir, Additional Superintendent of Rajshahi PBI.
Kunio, 66, was gunned down on Saturday, five days after the killing of a 50-year-old Italian citizen in Dhaka's high-security diplomatic zone.
Prime Minister Sheikh Hasina has indirectly blamed the Opposition BNP and its fundamentalist ally Jamaat-e-Islami for the murders.
With the arrest of the two persons today, the number of people held in the case has risen to four.
Earlier this week a former BNP leader and a businessman were remanded to 10 days in police custody for questioning.