Both are correct, they mean slightly different things. I would use the first to mean that he worked for a limited time in Ankara about two years ago, and that time ended. The second one means that two years ago, my father was at that time working in Ankara, and he may or may not still be working there to this day.

I prefer the first example. But both are suitable depending on the context.

"True" means factual or in reality. So, you must ask your father about what he was doing two years ago. ;) You mean to ask, "Which one is correct?" (this is a different question) By itself, "My father worked in Ankara two years ago" is the better choice. "My father was working in Ankara two years ago" provides context for another action. So then you need to tell us what happened while your father was working in Ankara.