The search operations in several offices were carried out by officers from the BRDE economic crimes unit, the source said.
Kohler previously worked in the ministry as a senior civil servant, including as cabinet director to Macron during his time as economy minister between 2014 and 2016.
Anti-corruption prosecutors on Monday said they had opened an investigation into 45-year-old Kohler over his links to the Swiss-Italian shipping giant MSC.
The probe is focusing on whether Kohler had a conflict of interest during his time at the economy ministry due to his relationship with MSC, the biggest client of major French shipyard STX France.
Kohler worked closely with the company in several senior ministry roles despite his family link to its client MSC, which was founded by billionaire cousins of his mother.
Kohler left the ministry in 2016 to join MSC as finance director, while continuing to work as an advisor on Macron's presidential campaign in his spare time.
Macron's office has dismissed the allegations of wrongdoing, first revealed by investigative website Mediapart, as "completely unfounded".
The case is an unwelcome development for Macron, who is known to be very close to his chief of staff.
Leftist opponents have accused Macron, a former investment banker, of being too close to company owners, while the allegations against Kohler also add to a list of legal investigations targeting his allies.
Labour Minister Muriel Penicaud, who also worked with Macron while he was economy minister, is being investigated over an evening she organised in Las Vegas to promote French technology companies in 2016.
The contract to organise the event was not put out to tender, leading to accusations of favouritism which she denies.
Macron's close ally Richard Ferrand also had to step down from his ministerial post last June due to a probe over a property deal.
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