From Czechoslovakia there is:
Konec srpna v Hotelu Ozon (by Jan Schmidt)
It's more like post-apocalyptic Sci-Fi. Available only from Facets.
Vynález zkázy (by Karel Zeman)
It's made for children primarily, but certainly worth checking out. Most of Zeman's films are a little Sci-Fi.
Muz z prvnÃho stoletà (by Oldrich Lipsky)
This even got a nomination for the Golden Palm, but doesn't seem to be too great.
Ztracená tvár (by Pavel Hobl)
A comedy about switched faces. Probably not what your looking for, but still Sci-Fi.
Rekviem za rytierov/Requiem for a knight (by Jozef Zachar)
I think it's about time travelling knights. I haven't seen it, it's not listed on IMDB.
also, seemingly some-what Sci-Fi:
Blbec z Xeenemünde/
The Idiot from Xeenemünde and Tarzanova Smrt/
The Death of Tarzan (both by Jaroslav BalÃk)
These have Sci-Fi elements, but are set before WWII. I also haven't seen them, but have read the short story for the former.
The same director also made
Miss Golem in the 70s.
Then the later
ZÃtra vstanu a oparÃm se cajem also by Polák, is pretty hilarious Sci-Fi.
From the 70s there is also
Akce Bororo (by Otakar Fuka)
Don't know it, could be campy fun.
There are some later Sci-Fi, but otherwise this list is pretty complete for Czech films. Unfortunately most of them aren't available, not to mention with subtitles. But maybe you'll get to see them somewhere once...
)