Exit polls cited by local television said her wing of the Peronist party would not win in Buenos Aires province, home to 40 per cent of the nation's 30 million-plus voters.
It also stood to lose in the federal capital; the second city of Cordoba; and the cities of Santa Fe and Mendoza, the reports showed.
Opposition lawmaker Sergio Massa, mayor of Tigre and a former cabinet chief for the current president, defeated the Kirchner wing candidate in Buenos Aires province, the reports said yesterday after polls closed at 0230 IST.
While Kirchner's wing of the Peronists was likely to remain the single largest political movement at federal level, it was not clear by late Sunday if they would hold on to majorities in both houses of Congress.
More From This Section
Voters were eligible to cast ballots to elect half the lower chamber of Congress and a third of the Senate.
The standard bearer of the populist-nationalist Peronists, Kirchner is barred from running for a third term in 2015 and many see yesterday's vote as the start of the race to replace her.
A polarizing figure, Kirchner has seen her popularity sag in recent months, despite a health crisis which some thought might bolster her public support.
Her oldest son Maximo, said that Kirchner on Sunday was "well, and in good spirits" after surgery this month to remove a blood clot on her brain.
She was not, however, quite well enough to cast a ballot, and continues to rest and heal at the presidential residence north of Buenos Aires.
Mariel Fornoni, head of pollster Management & Fit, said the election was a key barometer of support -- or lack of it -- for the Argentine leader.
"It is a cycle that is ending, and a point of departure. Monday is the beginning of the race for the presidential election of 2015 and control of Peronism," Fornoni said.
Argentina's business class has been angered by Kirchner's failure to control inflation and protectionist economics, import restrictions, the nationalization of companies such as energy giant YPF and foreign exchange controls.