Progress M1-3 was launched by a Soyuz-U carrier rocket from Site 1/5 at the Baikonur Cosmodrome. Launch occurred at 16:26:42 GMT on 6 August 2000. The spacecraft docked with the Aft port of the Zvezda module at 20:12:56 GMT on 8 August. It remained docked for three months before undocking at 04:04:49 GMT on 1 November to make way for Soyuz TM-31. It was deorbited at 07:05:00 GMT on the same day. The spacecraft burned up in the atmosphere over the Pacific Ocean, with any remaining debris landing in the ocean at around 07:53:20 GMT.
Progress M1-3 carried supplies to the International Space Station. It was unloaded during the Space Shuttle missions STS-106 and STS-92, as the ISS did not yet have a permanent crew. The Expedition 1 crew arrived the day after Progress M1-3 departed the Station, using the docking port that it had vacated.
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.