I imagine that other countries had embassies in Berlin if they were not at war with the country, and especially so Japan. What happened to those personnel when the Soviets attacked the city?
First of all - during ww2, only the grand powers maintained embassies headed by an ambassador to each other. All other nations had a lower level of diplomatic representation, often a legation headed by a minister.
The Swedish legation in Berlin consisted of 1 minister, 4 military attachés and 8 other staff. The priest in residence in the Victoria parish, the Swedish lutheran church in Germany was also closely tied to the embassy (Three priests manned this position during the war and all Three made efforts to aid Jewish refugees).
A bunker was built on the legation grounds in summer 1943, which was used when the legation buildinds were destroyed in a fire as a result of allied bombings on the 22nd of November 1943. Most of the legation moved to the castle Alt Döbern 120km southwest of Berlin after the fire, but some activity remained in the bunker. During Spring 1945, the legation moved to the castle Friedrichsruh outside Hamburg.
The legation bunker was reached by Soviet Soldiers on the 1st of May. As far as I can find, the Soviets respected the diplomatic status of the Swedish personell in the bunker.
On the 18th of May 1945, the entire legation was with Soviet and Western Allied approval, withdrawn to Sweden.