The context was an badgering interview trying to make him denounce his father. He was obviously uncomfortable with entire line of questioning and gave ambiguous responses. Your piecing together a "denial" in this context is an attempt to read the man's soul.
You may think you have reason to suspect that Mel doubts the six million figure but to say the he "denied the Holocaust" is patently false.
Here is the relevant portion of the interview by Peggy Noonan, and Reader's Digest, along with the quote that our resident bigot has been misusing over and over.
RD: Your father. I have read in some articles that your father has some very conservative religious beliefs, and, according to at least one story, that he has questioned some of the accepted versions of the Holocaust. Is there anything you want to share about that?
Gibson: My dad taught me my faith, and I believe what he taught me. The man never lied to me in his life. He was born in 1918. He lost his mother at 2 years of age. He lost his father at 15. He went through the Depression. He signed up for World War II, went off to Guadalcanal, got malaria and shot at and didn't like it too much. Served his country fighting the forces of fascism. Came back, worked very hard physically, raised a family, put a roof over my head, clothed me, fed me, taught me my faith, loved me. I love him back. So I'll slug it out until my heart is black-and-blue if anyone ever tries to hurt him.
RD: You're going to have to go on record. The Holocaust happened, right?
Gibson: I have friends and parents of friends who have numbers on their arms. The guy who taught me Spanish was a Holocaust survivor. He worked in a concentration camp in France. Yes, of course. Atrocities happened. War is horrible. The Second World War killed tens of millions of people. Some of them were Jews in concentration camps. Many people lost their lives. In the Ukraine, several million starved to death between 1932 and 1933. During the last century, 20 million people died in the Soviet Union.