There have been assertions that the Vatican extended diplomatic recognition to Manchukuo. A number of nations did so (and I can't really speak to most of them) but the Vatican was not one of them. They did nominate a "representative ad tempus of the Holy See and of the Catholic missions of Manchukuo to the government of Manchukuo", but this was not an official diplomatic envoy. Instead of generating from the office of the Secretary of State (the normal office for such undertakings) it was from a religious body. Basically the Vatican wanted to have a voice that could deal with the de facto government without extending de jure recognition. So, while other nations did recognize Manchukuo (perhaps most notably Germany, Italy, and Spain), the Vatican used the loophole of being a religious body as well as a state and found a de facto solution to be able to communicate without extending a de jure recognition of Manchukuo.
Follow-up question: Wikipedia says the Soviet Union recognized Manchukuo in 1941. Why would the Soviet Union have done that, knowing that Japan was an ally of Nazi Germany and just 2 months before Barbarossa?