The Andean nation is a small producer of soybeans compared with its giant agricultural neighbors, Brazil and Argentina, but output and exports of the oilseed have jumped in recent years due to improved crop yields and bigger plantings.
Production should reach 2.4 million metric tons (2.6 million tons) this year, of which about 80 percent would be exported, industry groups say.
Virtually all Bolivian soy uses GM seeds and the law signed by Morales earlier this month has rattled growers in the lowland east, historically a bastion of opposition to the Aymara Indian president -- a vocal advocate of organic farming methods and Pachamama, which means Mother Earth in the Andes.
The legislation, which former coca farmer Morales has called a means "to live in equilibrium and harmony with Mother Earth," also calls for limits on the expansion of farming into new areas and assigns a spiritual value to land beyond its social and economic function.
Soy plantings are due to start in earnest in Bolivia's lush lowland plains in the next few weeks, but some industry figures say uncertainty over the new rules could affect farmers' plans.
"It's possible with this uncertainty that some people will avoid sowing or sow less using any non-GM seeds they can get hold of," said Fernando Asturizaga, an advisor from the Anapo farming association based in the eastern city of Santa Cruz.
Agricultural leaders are holding talks with the government to call for changes to the GM ban and express broader concerns about the legislation. A second meeting between farm groups and officials was due to take place on Wednesday.
"We want them to understand the potential consequences of the measures contained in the Mother Earth legislation and to make changes or clarifications either in the implementation of this law or through a new law," Asturizaga said.
Soy exports brought in about $800 million last year, making the oilseed the country's third-biggest foreign currency earner after minerals and natural gas, according to the Bolivian Foreign Trade Institute (IBCE).
Most of the shipments went to Venezuela and other Andean countries in the form of soyoil and soymeal.
Growers say the new regulations may also threaten the production of other crops such as corn, sugar, rice and sorghum which farmers use in rotation with soybeans. They say that could drive up food costs in South America's poorest country.
The GM ban, which would take effect gradually under the law, could also compound the impact of high transport costs in the landlocked country that make it harder to compete, critics say.
"It's like running the 100-meters but shooting ourselves in the foot first. We're giving our neighbors too many advantages," said Marcelo Traverso, president of the APIA agricultural suppliers' association.
"It's a big step backwards that's going to have serious economic repercussions for the Bolivian farmer."
(Editing by Chizu Nomiyama)