Rolls-Royce said at the time that it could face prosecution over the allegations.
"We have been informed by the Serious Fraud Office that it has now commenced a formal investigation into these matters," Rolls-Royce said on Monday.
Shares in the company were down 0.1 percent at 1041 London time, lagging Britain's blue-chip index which was up 0.4 percent.
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"This is just the next step in the process," Liberum analyst Ben Bourne said of Rolls-Royce's announcement.
The SFO has been reviewing the findings of Rolls-Royce's internal probe since earlier this year.
Tommy Suharto, the youngest son of Indonesia's late president, in November denied allegations that he received bribes from Rolls-Royce.
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A source familiar with the matter said last December that the allegations related to the "distant past".