Following the Paris Peace Agreements in 1991 and the return of Norodom Sihanouk to Cambodia, Chakrapong left FUNCINPEC to become Deputy Prime Minister of the State of Cambodia and a member of Prime Minister Hun Sen's Cambodian People's Party (CPP) central committee.
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In 1999, he was granted pardon by the King with Prime Minister Hun Sen's agreement and returned to Cambodia where he founded a private airline: Royal Phnom Penh Airways which operated until late 2005.