The name of Fabrice Aidan, a middle-ranking French diplomat who was seconded to the United Nations from 2006 to 2013 and later worked at the bank, appeared in more than 200 documents released by the US Justice Department.
These include emails he is alleged to have sent Epstein between 2010 and 2016 from his personal and UN accounts.
Some of the emails reviewed by Reuters show the transfer of UN Security Council briefings and other confidential documents to Epstein during that period.
Aidan has denied wrongdoing.
The French foreign ministry has also begun an administrative investigation and disciplinary proceedings against Aidan. The ministry and Aidan's lawyer did not immediately respond to requests for comment.
The search was carried out on Friday in the presence of Ariane de Rothschild, the Swiss bank's boss, a source close to the bank said.
Edmond de Rothschild was cooperating fully with the justice system in the investigation led by the financial prosecutor, the same source said, adding that an internal inquiry had been launched as soon as suspicions emerged concerning the former employee, who worked at the bank from 2014 to 2016.
A spokesperson for the bank declined to comment.
The investigation is being led by officers from France's central office against corruption and financial and tax offences, which questioned Aidan in a voluntary interview in late February.
The French financial prosecutor's office said it was investigating accusations of passive corruption of a foreign public official and complicity in that crime, targeting Aidan in particular.
Ariane de Rothschild also appeared in the files released by the US Justice Department in January, which showed she kept up a years-long personal correspondence with Epstein before his 2019 arrest.
After the files were released, a spokesperson for the bank said that Epstein was a business acquaintance of de Rothschild from 2013 to 2019. De Rothschild had no knowledge of Epstein's conduct, the spokesperson said.
