Recovery in these troubled times isn’t easy for Japanese auto makers, bruised and battered earlier this year by natural calamities.

A new Goldman Sachs Japan report says although the impact from recent flooding in Thailand is limited, auto industry managers in Japan clearly have a sense of crisis concerning the global economic slowdown and strong yen, now hovering at ¥77/$1. Yet the outlook is basically upbeat.

Even assuming a foreign exchange rate of ¥75/$1, GSJ analysts believe strong growth in Japan’s auto sector is likely next year, with Toyota and Honda expectations high and Nissan and Daihatsu at a relative advantage with their emerging-markets strategy and localization.

A cautionary note emphasizes that not every auto maker will see high profits when growth is low in the developed world and steady in the emerging world.

“Japanese auto production volume is fluctuating widely due to the impact of the earthquake and Thai flooding, and fundamental demand is generally low,” says GSJ senior analyst Kota Yuzawa. “Actual demand is difficult to gauge due to production constraints brought on by the double impact of the natural disasters.”

So far, the level of recovery varies significantly by maker.

Honda and (Fuji Heavy Industry, maker of Subaru) have been knocked off course by supply constraints,” he says. “Honda has been the hardest hit by the Thai floods and is confronting related production constraints.

“FHI is attempting catch-up production but is already operating at high utilization. We expect continued inventory shortfalls for both at the end of 2011, when most other makers’ inventory is returning to normal. But both are rebounding and have been regaining share in the U.S. market, the source of half their profits.”

In the current fiscal year ending March 31, for example, GSJ sees Honda’s global sales dropping 251,000 units, compared with like-2010, to 3.26 million before rising to 3.63 million and 3.8 million, respectively, in the next two fiscal years.

For Toyota, “the strong yen is a major obstacle in the way of profits near term,” Yuzawa says.

The auto maker’s underperformance stands out among competitors as it struggles to achieve high earnings despite troubling foreign exchange levels, even taking quality-assurance costs into account, and he questions whether price hikes are likely to penetrate deeply.

Toyota’s global sales are expected to rise about 1% to 7.38 million units this fiscal year and recover to 7.63 million and 7.97 million, respectively, in the next two fiscal years.

Underscoring its current plight, Toyota announced after the Goldman Sachs Japan report was completed that the company expects an operating profit for the current fiscal year of ¥200 billion ($2.6 billion). The revision is 44% below its previous forecast made in August of ¥450 billion ($5.8 billion).

Mazda is another underperformer, with the strong yen shrinking exports and causing low utilization at the auto maker’s Flat Rock, MI, joint-venture plant with Ford, squeezing North American earnings. Mazda announced earlier in the year it would end production of the Mazda6 at the facility and move it to low-cost Mexico.

Unlike competitors that have taken a full hit from natural disasters, both Nissan, with 35% of its profits from China last year, and Daihatsu, with 40% of its profits from Indonesia, may grow their operating profits more than 10% in the next fiscal year.

For the current fiscal year, Nissan’s global sales are expected to climb 10% ahead of like-2010 to 4.28 million units and continue rising to 4.4 million and 4.8 million, respectively, in the next two fiscal years.

Goldman Sachs Japan is forecasting modest increases in global auto sales of 3% to 74.3 million units this year, 5% to 78.3 million next year and 6% to 82.7 million in 2013. The number will jump to 107 million in 2020, with most of the growth, or 71.4 million, coming from the world’s developing markets.

In the years ahead, barring more natural disasters or other unforeseeable calamities, GSJ says Japanese auto makers are expected not only to regain their health but also their share of the total global market, which traditionally has been about 30%.