The charity says its own sources on the ground report "untargeted fire resulting in civilian deaths" in the city of Fallujah.
It also blames coalition forces for obstructing lifesaving supplies such as food and medicine by holding them up at checkpoints and stopping civilians from seeking safety outside the city.
Doctors have estimated that more than 600 Iraqis have been killed in Fallujah since the American siege began in April.
Merlin also condemned the US Marines for using Fallujah's general hospital as a military base.
In a statement, the charity said: "We urge that all warring factions in Fallujah respect the Geneva Conventions and take every effort to avoid civilian casualties while facilitating their access to aid."
The statement was originally intended as a joint statement from UK-based NGOs in Iraq, but in the end only Merlin went public.
Earlier this month, the NGO Co-ordination Committee in Iraq sent a letter to the American administrator in Iraq, Paul Bremer, condemning the assault on Fallujah. "NGOs in Iraq have witnessed violations of the rights in the Geneva Conventions on numerous occasions," the letter said.