Alves was tourism minister under President Dilma Rousseff and Temer, who assumed the country's top post a year ago when Rousseff was removed for illegally managing the federal budget.
If found guilty, Temer is expected to appeal and delay the process for months.
The opening of unrelated probes into corruption allegations has led to hopes among Temer's opponents - and fears among his defenders - that the TSE could seize the opportunity to bring him down.
Adding to calls for his resignation or impeachment, the country's largest circulation daily, the Folha de S.Paulo, recommended in an editorial on Sunday that the TSE invalidate the Rousseff-Temer ticket and that he be removed from office.More news: Venus falls in fourth round at French Open
An agent of the Brazilian Federal Police does a security sweep with a dog, inside the chambers of the Superior Electoral Court, in Brasilia, Brazil, Tuesday, June 6, 2017.
Late on Monday, police sent Temer a list of 84 questions related to the allegations.
But starting Monday and until Thursday Temer faces the separate, more immediate challenge of the Supreme Electoral Tribunal, TSE, which is deciding whether abuse of power - principally the use of corrupt campaign money - fatally undermined the validity of the 2014 election in which Temer was reelected vice-president with then-president Dilma Rousseff. He has 24 hours to complete the document, but also a legal right not to respond, supreme court sources said.
Henrique Eduardo Alves was taken into custody on allegations of corruption related to the construction of a 2014 World Cup stadium in Natal.
Temer has refused to resign after the Supreme Court late last month authorized an investigation of the president for alleged corruption, criminal organization and obstruction of justice based on a secret recording of a conversation with a JBS executive in which he appeared to agree to the payment of hush money to silence a key witness in a massive graft scandal.More news: Shooting at parliament wounds security guard
Either or both parties can appeal a decision directly with the TSE which would have to rule within three working days.
On Saturday, Temer's former aide Rodrigo Rocha Loures was arrested on bribery charges. The president's lawyer Gustavo Guedes reiterated his client's statement of innocence before the court, saying: "President Michel Temer did not carry out any illegal acts".
According to the PSDB the Rousseff-Temer presidential campaign is guilty of abuse of political and economic power, obtaining campaign donations from companies involved in the Lava Jato scheme and bribing Petrobras executives for contract benefits.
If Temer is stripped of office, the Constitution determines that the president of the lower house, Rodrigo Maia, takes up the presidency for 30 days before Congress elects an interim president.
Janot is also rumored to have more evidence compromising the president, and further suspects in the corruption scandal could strike plea bargains and testify against Temer.More news: Arab nations cut ties with Qatar, saying it backs terror