In 1991, Chakrapong left Funcinpec to join the Cambodian People's Party (CPP) and served as the Deputy Prime Minister of Cambodia between 1992 and 1993.

When the Khmer Soul Party failed to win a single parliamentary seat in the 2003 general elections, Charkapong rejoined Funcinpec and briefly served as Senator in 2005.

Chakrapong was against the decision to co-opt the Khmer Rouge into playing any role in future Cambodian governments, a stand that came into conflict with Ranariddh and other senior Funcinpec leaders.

He was given a seat in the party's politburo,[11] and in January 1992 Chakrapong was appointed Deputy Prime Minister in charge of civil aviation, tourism, industry, culture, education, and social welfare affairs.

[14] On 10 June, Chakrapong led a few senior CPP allies, including Sin Song and Bou Thang, to declare the secession of seven eastern Cambodian provinces bordering Vietnam from control by the United Nations Transitional Authority in Cambodia (UNTAC).

Three days later, Ranariddh returned to Cambodia to preside over an emergency parliamentary meeting to reinstate Sihanouk as the country's Head of State.

At the same time, Tea Banh issued a directive to the Royal Cambodian Armed Forces to restore order in the seven eastern provinces.

Chakrapong obeyed his father's request to return and was awarded the military rank of Major-General for the Royal Cambodian Armed Forces.

[15] After a permanent government was formed in September 1993, Chakrapong and Sin Song appealed to the CPP politburo to be reinstated as Members of Parliament.

In May 1994, the CPP was able to secure support from Funcinpec to outlaw the Khmer Rouge in exchange for an agreement not to pursue any further motions to reinstate Chakrapong and Sin Song as Members of Parliament.

When Chakrapong heard that Sin Song was arrested,[16] he became worried for his life and safety, and sought refuge at Regent Hotel in Phnom Penh on 3 July.

Chakrapong called American journalist Nate Thayer for help, who assisted him to negotiate with government ministers and diplomats for safe passage out of Cambodia.

[17] Chakrapong issued a statement to deny his involvement in the coup attempt, and sent a letter to then-Malaysian Deputy Prime Minister Anwar Ibrahim for long-term asylum in Malaysia.

Chakrapong abstained from playing an active role in the party to avoid renewing tensions with his brother, and focused on his business career.

[21] Two months later, Ranariddh appointed him secretary-general, but faced opposition from some senior party members such as Nhek Bun Chhay and Lu Laysreng.

Nhek Bun Chhay followed the issue closely and provided a list of party members who were planning to defect from Funcinpec, which included Serey Kosal and Chakrapong.

[28] After Ranariddh sought exile in Malaysia in March 2007 following his conviction over his embezzlement charges,[27] Chakrapong served as the party's acting president.

[34] In October 2003, the director of Battambang Airport, Prum Chantha, reported that Royal Phnom Penh Airways had accumulated $1 million in unpaid taxes.

[35] Royal Phnom Penh Airways had already become bankrupt by March 2006 when the government presented Chakrapong a bill of $1.36 million in unpaid taxes, navigation, and landing fees.

In the 1990s, a public debate on ensued in Cambodia over the succession to the royal throne after Sihanouk was diagnosed with multiple health problems.

[40] Julio Jeldres, Sihanouk's official biographer, expressed in 1999 that Chakrapong had little chance of becoming the next king due to his alleged involvement in the 1994 coup attempt.

[41] In August 2002, Chakrapong raised the idea of holding national elections to choose a successor, and expressed concern over political interference in the Cambodian throne council.