Communist daily L'Humanite on Thursday said Muriel Penicaud had banked €1.13 million ($1.32 million) in 2013 from the sale of shares in food giant Danone where she was head of human resources.
The transaction was not illegal, but comes at a sensitive time for egalitarian France's new government. President Emmanuel Macron has announced deep public spending cuts and is showcasing his cabinet as a fresh start in a scandal-tainted political scene.
"If there is anything that leaves a stain on the public's confidence in the government, this is it," hard-left lawmaker Francois Ruffin said in the lower house of parliament, the National Assembly, on Friday.
Around the time of the sale, Danone had made 900 employees redundant.
Penicaud told Le Figaro newspaper: "Everyone has the right to express an opinion on the level of pay.
"However, I want to make it clear that the stock options were given well before the voluntary redundancy plan was announced and have no link to this. So I can only regret the efforts being made to link the two issues."
Government spokesman Christophe Castaner tried to take the air out of the controversy by saying that Danone's shares had risen in value since the minister sold them.