The move follows an alert from France's campaign finance oversight body this month, after it was unable to determine the sources of a total of 144,000 euros ($164,000) given to Macron's Republic on the Move (LREM) movement.
The funds were contributed via checks, bank transfers or electronic payments, the source said, confirming a report on Europe 1 radio.
Investigators want to verify that none of the donors exceeded the 7,500-euro annual limit on individual donations to political parties.
The inquiry comes just weeks after leftist firebrand Jean-Luc Melenchon was questioned and his home and party's headquarters raided in connection with two funding probes.
Melenchon denounced the inquiry as a “political manouevre” piloted by Macron, whose economic policies he has fiercely contested as leader of the France Unbowed party.
“Will there also be searches at his home? Membership and donor lists seized as well? Or will this openly be a case of double standards?” Melenchon wrote on Twitter on Tuesday.