The issue comes amid the worst crisis between Moscow and the West since the fall of the Soviet Union, following Russia's widely condemned annexation of Ukraine's Crimea peninsula.
"This trade ban has exposed the EU farming sector to significant losses," the European Commission said, adding that Russia's decision in January to close its market to live pigs and pork products had cut off almost 25% of all EU exports in the sector.
"After weeks of talks with our Russian counterparts to try to resolve this issue, we see absolutely no progress," said EU Trade Commissioner Karel De Gucht, giving the bloc "no choice anymore but to pursue this case at the WTO."
"This disproportionate ban is having a major financial impact on our European pig industry and cannot go unchallenged," added EU Health Commissioner Tonio Borg.
The bloc exports 700,000 tons of pig meat to Russia each year, according to the commission. The sales are worth EUR 1.4 billion (USD 1.9 billion dollars) annually.
Four cases of African swine fever have been detected in the EU this year, two in Lithuania and two in Poland, and all near the border with Belarus. Brussels has charged that the outbreak originated in Russia, reaching the EU via Belarus.
The European Commission has repeatedly argued that Russia is failing to live up to its WTO commitments, after joining the trade body in 2012.
It accused Moscow on Tuesday of "double standards," since it was accepting imports from Belarus and had done so until recently from Ukraine, "despite notified cases of African swine fever in these countries."
As reported, this past February, the Latvian government allocated a total of EUR 1,352,949 from the state budget's emergency funds to the Finance Ministry, the Agriculture Ministry and the Interior Ministry for African swine fever prevention measures.
African swine fever has never been registered in the territory of Latvia.
The Agriculture Ministry received information regarding the outbreak of African swine fever in southern Lithuania on January 24.