I'm no expert in soybean economics. I follow rice dynamics more diligently than that of soybean. The only research I have done regarding soybean is one in which we (Patunru, Trialdi and Havidz, 2005) looked closely into its price transmission across production and consumption centers (provincial levels with East Java being the reference market). The study found that prices across main provinces were in general weakly integrated, and some were not integrated at all in the long run. The study concluded that soybean price transmission (at least in 1993 to 2003) was constrained. In other words, the market was less than efficient.The possible causes of this were 1) weak marketing institutions, 2) poor infrastructure (esp. that to support distribution), and 3) inability of local farmers to match the international price. The latter came with qualification as the transmission from international to domestic price was also far from perfect.
Recently, there has been a big fuss over the increase of soybean price.
Kompas ran a couple of articles and op-eds. The tone, as you would have predicted, was of course to blame it on the government and liberalization. The observers cited there were both confused and confusing. Take this article for example. A parliamentarian reportedly said that the removal of import duty was absurd, because it "would not have any effect on price and the current shortage of soybean". He called it an "empty policy". But later in the article he was quoted as suggesting that the government should create incentive in the form of "high tariff when price is low and low or no tariff when price is high". That is exactly what the government just did (assuming of course that the "tariff" and "price" written by Kompas journalist mean import duty and world price, respectively).
The President, on the other hand, said that tempeh and tofu (both use soybeans as key ingredient) makers needed to adapt to the increased price. Sure. But then he went on with "the government will look for cheaper imports". His work would be much easier if he let the private sectors do the job. In fact, importation has been exclusive for only four big companies. Removing import duty might not be very efficient if the limited number of importers could collude to fix the price. The notion as said by one source that the "price crisis" is a result of "too much import" is foolish. The more you import the larger the quantity in the domestic market and the pressure to price is to take it down -- the magnitude of which depends on other things, e.g. distribution. The study on price transmission suggested that distribution is problematic, too.
So what's to do? In the short run, more, not less, import should be allowed. In the longer run, distribution and production problems are to be tackled. That includes improvement of road infrastructure and irrigation, as well as technology that leads to better varieties and farm management.