Rivera had worked at Youth With A Mission's University of Nations' campus in Kailua-Kona when he lied in email communications with school officials about the cost of construction and maintenance projects.
He faces a prison sentence of up to 20 years and a maximum fine of $250,000 at sentencing in August. He also must pay back the nearly $3.1 million he stole.
He will forfeit money and property the government has identified as proceeds from crime.
The government says Rivera stole the money from around September 2014 to this past January.
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