After the 2006 coup, many of Thaksin's economic policies were ended, the OTOP program was rebranded, the Government Lottery Office's program was deemed illegal, and the government nationalised several media outlets and energy companies. However, economists from the Thailand Development Research Institute (TDRI) published a report indicating that many of the populist policies had not boosted the economy and some were by coincidence.
After the 2006 coup, the military junta appointed a committee to investigate the anti-drug campaign. Former Attorney General Kanit Na Nakorn led the committee. Concerning the committee's results The Economist reported in January 2008: "Over half of those killed in 2003 had no links to the drugs trade. The panel blamed the violence on a government 'shoot-to-kill' policy based on flawed blacklists. But far from leading to the prosecutions of those involved, its findings have been buried. The outgoing interim prime minister, Surayud Chulanont, took office vowing to right Mr Thaksin's wrongs. Yet this week he said there was insufficient evidence to take legal action over the killings. It is easy to see why the tide has turned. Sunai Phasuk, a researcher for Human Rights Watch, a lobbying group, says that the panel's original report named the politicians who egged on the gunmen. But after the PPP won last month's elections, those names were omitted."
After the 2006 coup, the military junta-appointed Assets Examination Committee froze Thaksin's assets based on charges of policy corruption.
On 23 January 2006, the Shinawatra family sold their entire stake in Shin Corporation to Temasek Holdings. The Shinawatra and Damapong families netted about 73 billion baht (about US$1.88 billion) tax-free from the sale, using a regulation that made individuals who sell shares on the stock exchange exempt from capital gains tax. Thaksin was the target of accusations of corruption for selling forbidden national assets such as national utility company to a foreign entity in exchange for personal profits and kickbacks. Thai laws at the time disallowed the sale of integral assets of national importance to the public or to any foreign entity, but Thaksin amended the laws to allow such sale.
Thaksin announced the dissolution of parliament on 24 February 2006. General elections were scheduled for 2 April.
Thaksin had announced on 4 April 2006 that he would not accept the post of prime minister after parliament reconvened, but would continue as caretaker prime minister until then. He then delegated his functions to caretaker Deputy Prime Minister Chidchai Wannasathit, moved out of Government House, and went on vacation.
On 8 May 2006, the Constitutional Court ruled 8–6 to invalidate the April elections based on the awkward positioning of voting booths. The ruling was called a landmark case in "judicial activism". The Democrat Party, which had boycotted the April elections, said they were now ready to contest an October election.
Protests by the People's Alliance for Democracy massed in 2006, and on 19 September 2006 a military junta which later called itself the Council for National Security (CNS) replaced Thaksin's caretaker government in a coup while he was abroad. The Constitutional Tribunal dissolved the Thai Rak Thai party for electoral fraud ex post facto, banning him and TRT executives from politics for five years. The CNS-appointed Assets Examination Committee froze Thaksin and his family's assets in Thailand, totalling 76 billion baht (US$2.2 billion), claiming he had become unusually wealthy while in office. Thaksin and his wife had declared assets totalling 15.1 billion baht when he took office in 2001, although he had transferred many of his assets to his children and associates before taking office.
On 2 October 2006 Thaksin and his former deputy Somkid Jatusipitak resigned from the TRT. Chaturon Chaisang took over as party head.
On 31 December 2006 and 1 January 2007, several bombs exploded in Bangkok, killing three and wounding a number of bystanders. Prime Minister General Surayud Chulanont accused "those who lost power as a result of the military takeover" of masterminding the bombings, but did not directly identify Thaksin. Thaksin went on CNN to publicly deny any involvement in the bombings. The government did not make any arrests in the case.
Thaksin's diplomatic passport was revoked on 31 December 2006 after the junta accused him of engaging in political activities while in exile. Thai embassies were ordered not to aid him in his travels.
The judges decided to seize 46 billion differences in value of Shin Corp. shares from the date when he came to office and the value when the shares were sold to Singapore's Temasek Holdings in early 2006. Note that, Thaksin had declared around 500 million baht in assets and Pojaman had 8 billion to 9 billion baht while Thaksin served as prime minister. Nevertheless, during that period, Shin shares gained 121%, compared with a 128% gain in the benchmark SET index, while Siam Cement, one of Thailand's premier blue chip companies, gained 717%. The judges did not find that Thaksin was guilty of malfeasance. They also noted that any benefit to the government from Thaksin's policies was irrelevant to the ruling. The government reaped approximately 100 billion baht in increased revenue from changes in the concession agreements alone.