The company's sales for the quarter and fiscal year were nevertheless boosted by stronger results from its corn products, as well as higher sales of its Roundup and other glyphosate-based herbicides.
But the lower than expected fourth quarter loss resulted in Monsanto's shares falling 5.3 percent, or $2.46, to $43.95 on Wednesday.
The agricultural products firm saw fourth quarter sales of soybean seeds and traits drop to $27m, compared to $62m in the previous year. The company's sales of other crop seeds and traits also fell to $138m, compared to $154m last year.
This brought total sales for Monsanto's seeds and Genomics business down to $532m, from $545m in the company's fourth quarter last year.
The company said the lower results were partly a result of a higher percentage of its annual sales in the first nine months of 2006, compared with sales in the same period in 2005.
Monsanto also said it was facing challenges in Brazil and India, two of its large growth markets, and will be taking steps to achieve further market penetration.
According to the firm's chairman, president and CEO Hugh Grant, Monsanto is on track for double-digit growth over the next year, partly due to the steadily improving market penetration of its biotech crops.
Total net sales for the fourth quarter of fiscal 2006 stood at $1.4bn, representing a 9 percent increase from last year. For the full year, the company reported sales of $7.3bn, 17 percent up from 2005.
Full-year results were boosted by sales from acquired businesses, with 2006 being the first year that Monsanto recorded a full year of sales from its Seminis and Stoneville businesses, both of which were acquired in 2005.