Temer, the first president in the country to face criminal charges while in office, is accused of obstruction of justice and racketeering.
The charges have gone before the lower house of Congress, which must decide whether to vote for a trial in the Supreme Court, in which case Temer would step down for 180 days.
Temer, who has been courting legislators for days to ask for them to vote against a trial, delivered his statement for the defense via his lawyers.
"Based on a confused and improbable narrative, the complaint lodged against the president of the republic by the Federal Public Ministry is inept. It is a farce in the form of prosecution," lawyers for Temer said.
They said that the case was based "exclusively" on plea bargains struck with "confessed criminals" without any credible documentary evidence.
Next, the charges will be debated and voted on by the lower house justice committee.
The committee's recommendation would then go to the full house, where 342 of 513 deputies would have to vote against Temer for him to be put on trial. Any less and the charges would be thrown out as long as he remains in office.
Temer already defeated a first charge of bribe-taking when the lower house overwhelmingly voted against a trial in August. Analysts say he now has at least a strong majority to combat the new charges.
However, the scandal has weakened Temer's ability to pass tough austerity reforms, particularly a tightening of the country's generous pension system.
It has also made him the most unpopular leader on record. A poll in September found that only three percent of Brazilians think his government is doing a good or very good job.
The latest charges involve Temer's alleged agreement to pay hush money to keep a jailed politician from testifying and his leadership of a group in Congress that took millions of dollars in bribes from companies seeking state contracts.
According to the charges, Temer "acted as leader of a criminal organization" comprising senior officials from his center-right PMDB party. They allegedly took the kickbacks in exchange for contracts at public companies like oil giant Petrobras.
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