The crash on July 18, 2009, injured 48 people and caused $4.5 million in damage.
NTSB investigators said in the report that the crash was caused by Henry Gray, the operator of an L-Taraval train that struck a stopped K-Ingleside train as it pulled into the station.
Gray had switched the train into manual mode 24 seconds before the crash and said he had then briefly lost consciousness because of a medical problem, according to the report.
NTSB officials determined that Gray's blackout was likely caused by aortic stenosis, the narrowing of an outflow valve of the heart.
The accident was also the fault of the San Francisco Municipal Transportation Agency for its "failure to monitor and enforce" safety rules that could have prevented the accident, the report stated.
The report found that prior to the 2009 crash, Gray was involved in five previous light-rail incidents after being transferred to that division in 2006, including another crash at the West Portal station in 2007.
Gray was suspended for five days after the 2007 accident, which Muni determined could have been avoided.
In both West Portal crashes, the train had been put into manual mode, which was a common time-saving practice among Muni operators.
The agency's work rules require train operators to notify the control center before switching from automatic to manual mode, but the NTSB report found that operators frequently made the switch without permission.
According to data collected by Muni, about 40 percent of operators switched from automatic to manual mode before reaching the West Portal station's platform between July 2008 and July 2009.
Two days after the 2009 crash, Muni officials issued a bulletin reminding operators that they could face serious consequences if they failed to get permission before switching to manual mode.
In the year before the crash, the monthly average of trains entering the West Portal station while it was occupied by another train was 2,635, but after Muni sent out the bulletin, that number dropped to fewer than 10 over the next several months.
Muni spokesman Paul Rose said agency officials were looking at the report this morning and would issue a statement about it later today.