You've just learned that one of your previous employers has been giving you a bad reference. Count your blessings that you found out, because many never do. But what do you do about it?
Addressing the Problem
Your goal isn't necessarily to erase or debate the issue, only to reach agreement on its presentation.
When you phone your reference, prevent them from becoming defensive by saying, "I'm calling to ask your help with something. I understand you have an issue with my performance when I worked for you, and I'm wondering if we might be able to reach an agreement on how it's presented, so that it doesn't compromise my chances of employment. Would you mind sharing with me, please, what you weren't happy with when we worked together?"
Your tone of voice must be respectful, polite, and convey your desire for information and understanding. If you're angry, defensive, or whiny, or they perceive they're being attacked, you're not going to get what you want or need - information and cooperation. Creating an environment where they feel comfortable talking is more likely to open a conversation.
Don't argue, interrupt or react defensively. Just listen. And when they're done speaking, tell them you appreciate their sharing with you. This relaxes them further and moves you closer to a win/win agreement.
Negotiating the Message
Next, ask your reference what the positive aspects of your performance were. Ask if they'd be willing to share that information as well next time. Again, this is negotiation for a win/win, not an argument to win or lose. Make sure they realize you're not asking them to remove the negative, but simply to frame it in a less harmful light and balance it with the positive. When you approach the conversation with the goal of resolving the situation and healing the relationship as best it as can be healed, everyone usually wins.
Diffusing the Situation
As you continue interviewing, address this with a prospective employer before the reference is checked, but not until an offer is imminent. Assuming the issue is a valid one, acknowledge you've had some difficulty in the past, but since then it's no longer relevant (if this is true). Don't make excuses or try to explain. Now you've defused the situation and removed the element of surprise.
If there's no validity, you'll need to address that too. Perhaps by presenting the complaining supervisor as someone who was threatened, new, or who wanted their own person in your position, or whatever the case truly was. Be brief, objective, and balance it with a positive about the person as well. Trashing them reflects poorly on you and will backfire.
A wise word to every job seeker: contact your references before you start looking. Send them your resume. Tell them what you'll be interviewing for. Ask them what they might contemplate saying and how they'd speak to your abilities. Ask their permission to use them as a reference. References are sacred. Their privacy and willingness to speak on your behalf is to be respected and appreciated. A little homework such as this will prevent reference problems from occurring.