The latest update, which was designed to fix a face import bug, is causing the title to crash during the loading of the main menu, particularly on the Xbox 360 version.
The problem seems to occur during the game's attempts to contact the EA servers, leaving the title stuck in a continuous load cycle.
Players have had some success loading an offline game and clearing the cache, while others have fixed the problem by swapping discs, reports Eurogamer.
BioWare is aware of the problem and has appealed for help during its investigation.
Announced last month, the face import patch fixes a bug affecting the appearance of a Commander Shepard imported from the original game.
New patches are "heavily tested by BioWare, EA, Microsoft and Sony", explained BioWare's Chris Priestly.
He added: "If a patch fails during testing, it is sent back, fixed again and retested until it passes. Then it is released to gamers. Until we know that the patch has passed certification testing, I don't want to give even a rough idea of the date, to prevent disappointment should it need further testing."
The system crashes are the latest in a string of controversies surrounding the release of Mass Effect 3.
A campaign was launched to change the game's controversial ending, while some right-wing groups in America have criticised the EA and BioWare for including openly gay and lesbian characters.
Mass Effect 3 shipped 3.5 million copies worldwide during its first week on sale, making it the biggest entertainment launch of the year, according to publisher Electronic Arts.
Mass Effect 3 is available on Xbox 360, PS3 and PC.
> Read our review of Mass Effect 3
Watch the launch trailer for Mass Effect 3 below: