"Since our withdrawal (in December), it was our top priority to sell the team on condition it continues its F1 activities," the unnamed official told the Yomiuri Shimbun newspaper. "The price was not a problem," he continued.
"We could not sell the team to partners who had sought to disband it and sell its assets on a piecemeal basis," he said. "We also needed to protect the jobs of hundreds of people and we think it was a good conclusion."
A Honda spokesman declined to reveal financial details of the deal.
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Honda is reported to have spent £136 million in running the F1 team.
Honda's profit was estimated at £544m for the business year to March 31, down 87 per cent from the preceding year.
Brawn's Mercedes-powered team has won the first two Grand Prix this season through driver Jenson Button, in the Australian round and Sunday's rain-shortened race in Malaysia.
Button's team-mate Rubens Barrichello finished second in Melbourne.
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