Japan continues to be “our most challenging major market,” Apple CFO Peter Oppenheimer told analysts last month during the company’s fiscal fourth quarter earnings conference call.

That may be, but one of the numbers that jumps out of the Form 10-K that the company filed with the SEC on Wednesday is 39% — the percentage Apple’s net sales grew in Japan last year.

What makes that number remarkable is that it follows an 11% drop in net sales the year before.

Why the turnaround? According to the 10-K report, it was driven by sales of iPods, iMacs, MacBooks and “strong sales from the iTunes Store.” The report singles out Mac net sales and unit sales, which grew 42% and 20%, respectively.

Apple AAPL attributes the declines between 2006 and 2007 to general shrinkage in Japan’s consumer PC market and lower average selling prices of iPods.

The MacBook and MacBook Air contributed to the increase in net sales in fiscal 2008, as did strong demand for the iPod touch and iPod nanos at higher average selling prices.

Here are the numbers Apple provides:



The report does not mention sales of the iPhone in Japan, which after the initial excitement this summer are said to have slowed. See here.

According to the 10-K, “The company is continuing to evaluate ways to improve the future results of its Japanese segment.”