The elections, for half of the lower house and a third of the senate, are a test for Fernandez, who has seen her popularity drop since she succeeded her husband, Nestor Kirchner, as president 15 months ago.
A farming dispute has weakened her administration and Argentina's economy has been slowing after six years of growth. However, it is yet to suffer the mass layoffs and banking turmoil seen elsewhere.
The ruling party holds a majority in congress, but several high-profile figures have crossed the floor in recent months. Some left in protest at the government's handling of the farm conflict over soy export taxes.
Critics said the government was trying to cut short opposition efforts to form alliances.
Margarita Stolbizer, a leading opposition figure from the Civic Coalition party, said: "They're clearly trampling on the rules with this decision.
"The government has realised it's in a weakened position going into the election."
Fernandez's popularity was at 50 per cent when she took office in December 2007. Last month, only 29 per cent of Argentines had a favorable image of her, according to a poll by the Poliarquia consultancy.
In another sign of her administration's weakening hold on power, a ruling party alliance was comfortably defeated in local elections in the Andean province of Catamarca on Sunday.