Lemonde joined the tribunal in the office of co-investigating judges in 2006.
Defense teams and prosecutors both have 30 days to appeal the closing order, which came after three years of investigation.
Their trial is expected to start in the first half of next year. The suspects deny the charges against them.
The film won the Special Jury Prize at the Sundance film festival in January and has been released in the US, Europe and Asia.
Cabinet Minister Sok An on Tuesday urged representatives from 30 donor countries to consider more funding for the Khmer Rouge tribunal.
The tribunal has experienced cash-flow problems this year, with some donors reluctant to fund the court.
The appointment is expected to go to Rong Chhorng, who is currently the acting head of the unit.
Today this Buddhist temple is tranquil, but when the Khmer Rouge ruled Cambodia between 1975 and 1979, it was anything but.