The country's deputy trade minister also said on Friday that the country's beef import quota would inch up.
Although the moves are unlikely to have a major impact on international markets for soy and beef, they underscore investor concerns over the Indonesian government's increasing control over food markets in the country as it struggles to balance the interests of farmers and consumers.
The government has been criticised by international trading partners as it often uses import tariffs or quotas to protect domestic agriculture.
Indonesia, a country of 240 million which meets 70 percent of its annual needs of the oilseed through imports, now links traders' imports of soybeans to the volume of the oilseed they buy at home.
Although Indonesian soybean imports are relatively small compared to the world's top buyer China, as wealth increases and eating habits change, shipments are likely to steadily climb.
Total soybean imports into Indonesia will hit 1.8 million tonnes this year, according to industry estimates, while the main domestic harvest is in late August. Total Chinese soy imports last year were 58 million tonnes.
RAMADAN
Bayu Krisnamurthi, deputy trade minister of Southeast Asia's largest economy, said the floor on buying soybeans from farmers would be 7,000 rupiah ($0.72) per kg, while the price for selling to makers of tofu and traditional food tempe would initially be set at 6,800-7,200 rupiah per kg.
The price for selling soybeans to tempe and tofu makers will be determined monthly, he added, similar to the current palm oil export tax which uses benchmark prices from the previous month.
U.S. soybeans rose for a seventh straight session on Friday, to about $15.04-1/2 a bushel.
Chiefly used by makers of soybean-based staple foods tofu and tempe, major buyers include FKS Multi Agro Tbk and Cargill.
Indonesian producers of tofu and tempe threatened to go on strike ahead of the start of the Muslim fasting month of Ramadan last year, in a bid to reduce soybean prices.
As part of efforts to tackle rising global food prices, Indonesia temporarily scrapped its soybean import tariff and extended the role of state procurement body Bulog beyond rice in order to build bigger food stockpiles.
Registered soybean importers, including Bulog, will not have limits on shipment volumes, Krisnamurthi said.
Bulog will also be allowed to import an extra 3,000 tonnes of beef on top of the 80,000 tonnes 2013 quota set last year, to meet rising demand ahead of Ramadan.
Consumers have been critical of government food policies, after it slashed import quotas for beef, which then helped drive up prices in Java and caused a corruption scandal.
