In filings to the country's top court, Attorney General Rodrigo Janot accused Temer of paying hush funds to a former speaker of the lower Chamber of Deputies and to an operator of his political group. Janot also alleged that Temer led the criminal organisation that operates in Brazil's Congress and the executive branch.
Temer has repeatedly denied wrongdoing.
As a sitting president, Temer will only be put on trial if two-thirds of Brazil's lower house votes to suspend him from office.
In the latest accusations, Janot said that Temer led a criminal organisation since May 2016, when he assumed the presidency. Temer, then vice president, took over when President Dilma Rousseff was impeached and later removed from office for illegally managing the federal budget.
Temer "promoted, organized and integrated willingly and personally a criminal organization formed by more than four people, including public agents who abused their positions to commit crimes" to obtain advantages in the government and Chamber of Deputies, wrote Janot.
The operation was authorized by Brazil's top court and is part of an investigation of Agriculture Minister Blairo Maggi, who is suspected of bribing state lawmakers during his 2003- 2010 terms as governor of Mato Grosso.
Police also raided offices of eight state lawmakers and the mayor of the state capital, Cuiaba, in connection with the case. The investigation began after a plea bargain was struck with Maggi's successor as governor, Silval Barbosa.
A police statement did not say whether Maggi was present during the raid at his apartment in the national capital, Brasilia.
"There was never a move by me or authorized by me to act illegally in my administration's decisions or to obstruct justice," he said in a statement.
But in the decision to green-light the raids, Supreme Court justice Luiz Fux said there was "clear evidence" that Maggi also tried to obstruct justice by paying bribes to a former state government secretary.
Maggi is one of Brazil's wealthiest agro-business leaders, known as the king of soybeans. He was elected senator in 2011 and named by Temer to his Cabinet post in May 2016.
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