Gabriela Zapata is a top manager at a Chinese building firm which recently won government contracts in Bolivia.
No details of possible charges were given and no comment from Ms Zapata was immediately available.
Opposition media have accused Mr Morales of peddling influence linked to the firm - a claim he denies.
This week he lost a referendum aimed at allowing him to run for another term.
Mr Morales - Bolivia's first indigenous president - accepted defeat in the ballot.
He also said a dirty war was now being waged against him, asking a parliamentary commission and state auditors to investigate the contracts with the CAMC Engineering company.
Official results of the referendum show that 51.3% of voters rejected the proposal to change the constitution to allow Mr Morales to run for another term.
He has been in power since 2006 and his current term runs out in 2020.
Bolivian President Evo Morales' former lover has been arrested as part of an investigation into alleged corruption, the interior ministry says.