Depending on the context, both sentences are correct.

'So' is used when you have some reference. For example, imagine you are having a conversation with your friend. You agree to meet up the next day at 10 am to go to another friend's party, and your friend points out that you are late every time, and that he has had to wait 30 minutes for you in the past. To which, you reply, "Oh, I'm sorry. If I'm late tomorrow, don't wait so long. Just wait for 10 minutes, and if I don't show up, then you can go ahead and I'll reach there directly."

Here, as you can see, we had a reference of 30 minutes, which was a long time, so you said, "Don't wait so long".

But imagine the same conversation, where your friend points out that you are late every time, but doesn't mention how long he has had to wait in the past. You reply, "Oh, I'm sorry. If I'm late tomorrow, don't wait too long. Just wait for 10 minutes..."

Here, you didn't have a reference of what is called a 'long time', so you just say "Don't wait too long; just 10 minutes."

Hope this helps!