It is primarily becoming rarer for customers to choose organic milk.
"Factors that could affect sales are, for instance, the economic climate and that customers are focusing on cheaper products," Maria Smith, Ica's head of environment and social responsibility, told the Sydsvenskan newspaper.
Overall, sales of organic products have more than doubled at Ica since 2007, so this year has been an anomaly.
Axfood spokesman, Ingmar Kroon, believes sales are affected by the public debate around the environment.
"The climate change debate has been down for a couple of years. If the environment and climate change receive a lot of media attention, then that has an impact," explained Kroon.
"Considering the recent reports about a four degree temperature rise and the catastrophic impact of that, perhaps the debate will kick off again. Then organic sales could see a jump," he added.
Out of the big supermarket chains in Sweden, Coop has the largest assortment of organic products, with just over 2,500 items and a 5.5 percent sales rate. Louise König, Coop's head of sustainable development, said sales remained constant in 2012.
After investing in organic milk, aiming to double production from 10 to 20 percent by 2015, dairy giant Arla has had surplus of produce this year.
The company increased production by 12 percent in 2012, but total sales of organic milk in Sweden went down by seven percent.
Krav, the organization that develops organic standards in Sweden, hopes that supermarkets will start displaying organic produce more prominently in the shops.
"When products are displayed better we immediately see a growth in sales," Krav spokeswoman Kristin Kooper told Sydsvenskan.