It's a good question. It depends on what the speaker is trying to convey. For example, if I saw my friend John at work, and he bought a new car, then when I get home, I would say to my wife (if I had a wife) "John said he HAS a new car" because the "HAVING" is still relevant, true information.
If, however, I saw as I was leaving work, that John actually bought scooter. I would say to my gorgeous wife. ``John said he had a new car. What a liar``.
The short answer: If you don`t know more about the context EITHER WAY IS FINE!