Gauging the iPhone’s popularity in Japan is not easy.

Just ask Brian X. Chen. He wrote a piece for last April called Why the Japanese Hate the iPhone suggesting that despite the long lines that greeted the iPhone 3G last summer, the device was a big flop in Japan.

“Apple’s iPhone has wowed most of the globe,” he wrote. “But not Japan, where the handset is selling so poorly it’s being offered for free.”

Chen had to issue an apology to readers and two major revisions after his piece was torn apart in AppleInsider by Daniel Eran Dilger, writing under the byline Prince McLean, for getting initial sales estimates wrong and badly misquoting a couple key sources. But neither Dilger nor Chen had a good handle on how the iPhone was actually selling.

Which is why there was some interest this week in a survey of 2,300 Japanese retail stores conducted by the market research company BCN, reported by and picked up Friday by the English language TG Daily.

According to this survey, cellphone sales are plummeting in Japan but sales of smartphones have grown 80% in the past year, with Apple AAPL clearly in the lead.

The survey listed the top 10 bestselling smartphones cellphones in Japan. Heading the list at No. 1 was the 32GB iPhone 3GS. Second in line was the 16 GB model.

According to TG Daily, Apple has sold 1 million iPhones since July 2008 through Softbank, its exclusive Japanese carrier. But take that number with a grain of salt; it sounds suspiciously like the initial sales estimate that got Brian Chen in so much trouble last April.

No. 3 in the BCN survey is the NTT DoCoMo Aquos SH-04A, designed by Sharp. Research in Motion’s RIMM BlackBerry Bold came in No. 6. Rounding out the top 10 list were four smartphones made by HTC.

UPDATE: On Sunday, Asiajin’s Akky Akimoto published an analysis of the survey that provides more detail and context — and corrects several errors in the initial report.

The BCN ranking turns out to be a weekly top 10 list of bestselling cellphones (not just smartphones) for the June 22 to 28 — the week the iPhone 3GS went on sale in Japan — and it was the new iPhones, not the old, that were the Nos. 1 and 2 bestsellers in Japan that week. Curiously, the new iPhones also appeared on a BCN survey the week before they actually went on sale, coming in at No. 174 (32GB) and No. 189 (16GB), respectively.

You can see the original BCN list in Japanese here.

Photo courtesy of Information Architects.