Malaysia's 1MDB, once a pet project of Prime Minister Najib Razak who chaired its advisory board, is the subject of money-laundering investigations in at least six countries, including Switzerland, Singapore and the United States.
Justo was jailed for three years in Thailand in August 2015 after the police said he admitted to blackmail and attempting extortion of his former employer Petrosaudi, a Saudi Arabia-based oil and gas company and joint venture partner of 1MDB.
Justo leaked several confidential documents from Petrosaudi relating to its joint venture with 1MDB that were published by Malaysian and international media groups early last year, and formed the basis for the graft and money laundering probe.
His sentence was cut to two years by a royal amnesty in August, prompting the Swiss authorities to request his transfer to serve the remaining term back home.
Thai Justice Minister Gen Paiboon Koomchaya was quoted telling Malaysian state news agency Bernama that the decision to deny Justo's transfer was made "in accordance with Thai law".
The Swiss foreign office said it took note of the decision with "regret". "Switzerland has not yet been officially informed by the Thai authorities of the decision to refuse the transfer to Switzerland," it said in a statement to Reuters.
Justo's lawyer in Thailand, Worrasit Piriyawiboon, said his client was not extradited because he has less than one year of his sentence left to serve.
The decision to reject Justo's transfer to Switzerland came shortly after Malaysia's prime minister concluded a visit to Thailand. Both countries have denied any interference.
Najib's press secretary said in a statement late on Tuesday that no one from the Malaysian delegation raised any matter relating to Justo during the Thai visit.
"Malaysia does not sanction attempts to interfere with the internal affairs or judicial process of other countries," Tengku Sariffuddin said in a statement.
The US Justice Department filed lawsuits earlier this year seeking to seize more than $1 billion of assets allegedly siphoned off from 1MDB, founded in September 2009 to invest in strategic property and energy projects.
Najib has denied any wrongdoing and said Malaysia will cooperate with the international investigations.
More than 200,000 people marched through the streets of Kuala Lumpur in August 2015 calling for Najib's resignation over the 1MDB scandal, and another protest rally is planned for November this year.