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The investigation is part of the massive 'car wash' corruption probe into Petrobras that has seen top-level politicians arrested.
Prosecutors allege Glencore and fellow trader Trafigura had paid Petrobras oil traders off to get cheaper prices.
"Evidence shows that there was a scheme in which the investigated companies paid bribes to Petrobras' employees in exchange for favours, more advantageous prices, and gaining contracts more frequently," the prosecutors said.
Glencore's share price fell to an intraday low of £2.88 (US$3.68) per share after Reuters published the allegations, before recovering to over £2.90.
The company, which announced a management reshuffle on Monday, declined to comment on the allegations.
