Progress M-46 was launched by a Soyuz-U carrier rocket from Site 1/5 at the Baikonur Cosmodrome. Launch occurred at 05:36:30 GMT on 26 June 2002. The spacecraft docked with the Aft port of the Zvezda module at 05:36:30 GMT on 29 June. Prior to docking it was used to conduct tests of the Kurs docking system. It remained docked for three months before undocking at 13:58:49 GMT on 24 September 2002 to make way for Progress M1-9. It was deorbited at 09:34:00 GMT on 14 October. The spacecraft burned up in the atmosphere over the Pacific Ocean, with any remaining debris landing in the ocean at around 10:21:59 GMT.
Progress M-46 carried supplies to the International Space Station, including food, water and oxygen for the crew and equipment for conducting scientific research.
Payloads are separated by bullets ( · ), launches by pipes ( | ). Manned flights are indicated in bold text. Uncatalogued launch failures are listed in italics. Payloads deployed from other spacecraft are denoted in brackets.