Information from Swiss authorities proved the existence of the accounts.
Eduardo Cunha – seen as the architect of former President Dilma Rousseff’s impeachment – could now face arrest.
Dilma Rousseff was removed last month for moving funds between government budgets, which is illegal under Brazilian law.
During a bitter debate on September 12, Eduardo Cunha accused her supporters of seeking revenge against him.
Eduardo Cunha is also known as the “keeper of secrets” in Congress, where dozens of other politicians are also accused of fraud and has suggested he may cooperate with investigators into a wide ranging corruption scandal.
He is also being investigated by the Supreme Court for allegedly taking millions of dollars in bribes to secure contracts with state oil giant, Petrobras.
Petrobras is at the centre of a massive kickbacks scandal which cost the company $2 billion and has led to the arrest of dozens of lawmakers and top businessmen.
At least three businessmen have said under interrogation that they paid bribes to Eduardo Cunha, which they deposited in his overseas accounts.
Along with his seat, Eduardo Cunha has lost the partial immunity from prosecution that comes with being an elected representative.
In March 2015, Eduardo Cunha stated that he did not have “any type of account anywhere that is not declared on my income tax”.
However, the Swiss authorities later gave information to a corruption inquiry in Brazil stating that Eduardo Cunha and his wife, Claudia Cruz, were beneficiaries of secret accounts worth about $5 million.
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