President Lagos was attacked over the ailing economy
With 99% of the votes counted, Mr Lagos' "Concert" coalition was on course to keep an eight-seat majority in the lower house, down from 20 seats before.
In the Senate, where only half the seats were up for renewal, the government's one-seat majority was lost and control is now split 24-24 with the right wing opposition.
Correspondents said the close results would make it difficult for the government to press ahead with plans to amend the constitution, put in place under former dictator Augusto Pinochet.
The results were also seen as a boost for the conservative mayor of Santiago, Joaquin Lavin, whose Democratic Party led the opposition Alliance for Chile.
Mr Lavin, who lost to Mr Lagos by less than 1% in the 2000 presidential elections, is now seen as the main contender for the 2005 vote.
In the lower house elections, the government's coalition won 48% of the votes, down from the 50% it achieved four years ago.
The opposition increased its share of the vote from 30% to 44%.
Its strongest gains were among candidates for the Independent Democratic Union, a far-right party mainly made up of supporters of Mr Pinochet.
General Pinochet, 86, did not vote. His spokesman said the former ruler was in bed with laryngitis. The election was seen as the first major test for Mr Lagos's 19-month-old government, which is battling an ailing economy and 9.7% unemployment.
Policies defended
Mr Lagos' opponents say unemployment grew mainly because of government support for workers' rights that made firing employees more expensive.
The president blames Chile's economic troubles on an international crisis worsened by the 11 September attacks on the United States and a steep drop in the price of copper - Chile's main export.
Mr Lagos has said that Chile's economy will grow by about 3% in 2001 and that the country is much better off than many others, especially in Latin America.