"The charge is obstruction of justice" linked to the Petrobras oil company embezzlement probe, named Operation Car Wash, a spokesman for the justice ministry told AFP.
Lula was formally charged along with six others, including former senator Delcidio do Amaral, a former ally in Lula's leftist Workers' Party who is accused of Petrobras-related corruption and has turned state's witness.
Lula, as he is universally known in Brazil, was president from 2003-2010 and left office with massive popularity for social programs that lifted tens of millions of Brazilians from poverty.
Lula is alleged to have been at the center of the scheme. However, the charges on which he will stand trial are limited to allegedly attempting to obstruct the enquiry.
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Lula's spokesman issued a statement saying that the charges were flimsy.
"The defense argues that the charges are based uniquely on (evidence from) a plea bargain" with Delcidio, the statement said.
The development comes a week before the opening of the Rio Olympics which Lula was instrumental in winning for the city in 2009 while he was still president.
His handpicked successor Dilma Rousseff faces her own problems, with an impeachment trial set to culminate in late August, days after the Olympics end.
If the Senate votes by a two thirds majority she will be removed from office and her bitter political enemy Michel Temer, who is currently serving as interim president, will take over.
Rousseff is accused of breaking government budgeting rules, but has denounced the impeachment process as a coup in disguise aimed at putting Temer's center-right administration in power and destroying the Workers' Party.