On Friday evening, we noticed that books from major publisher Macmillan had disappeared from Amazon.com, but couldn’t explain why. The fact that Macmillan was a partner on Apple’s iPad, which should be a formidable competitor to Amazon’s Kindle, seemed suggestive, but again: We didn’t know.

Now The New York Times has an explanation. Citing an anonymous source “in the industry with knowledge of the dispute,” The Times said the removal was caused by a disagreement between Macmillan and Amazon over the pricing of e-books on the Kindle. Amazon insists that publishers charge $9.99 for most e-books, while Macmillan wanted to raise the price to $15. So the online retailer is “expressing its strong disagreement by temporarily removing Macmillan books.”

Meanwhile, Apple is allowing publishers to set the prices they want on the iPad’s iBookstore. The Wall Street Journal actually pressed Apple chief executive Steve Jobs on this issue at the iPad launch event, asking why someone would buy a $15 e-book from Apple when they could get the same book from Amazon for $9.99.

“The prices will be the same,” Jobs said, implying that Amazon will eventually be forced to adopt more flexible pricing models. If The Times is correct, Macmillan’s removal could signal the next stage in that battle.

Amazon and Macmillan still haven’t responded to emails asking for an explanation.