A man allegedly threatening commuters with a machete on a busy SkyTrain was shot by a VPD officer as horrified transit passengers watched the terrifying incident unfold.

The 29th Avenue SkyTrain station in East Vancouver was packed with commuters during Monday morning's rush hour around 8:15 a.m. when Transit Police tracked the man to a train car, and tried to keep him inside.

"They evacuated the train and the surrounding area, and closed the doors to the car, containing the man inside," the VPD said in a statement issued to media.

VPD officers were called in to assist, and arrived several minutes later, according to the force, who says "as negotiations continued, the man broke his way out through the closed train doors with the machete."

Vancouver police say the man was shot by one of its officers after refusing to "follow police directions."

Cell phone video obtained by CTV News shows the suspect walking up the stairs from the platform holding what appears to be a large knife. A gunshot is heard moments after the man approaches officers with their weapons drawn.

The suspect was taken to hospital, where he remains, although his current condition was unknown by Monday afternoon. He has not been publicly identified.

In addition to investigations launched by the VPD and Transit Police, B.C.'s Independent Investigations Office will be conducting its own probe.

Its investigators were deployed to the station and will be collecting evidence, interviewing witnesses and officers.

In a statement, spokesman Marten Youssef said the IIO's focus will be to determine if any officer committed an offence as a result of the shooting.

The IIO says VPD officers responded to the station just before 8:30 a.m. as Transit Police cleared passengers from the area and called for backup.

"According to police, the male did not comply with officers’ requests and was subsequently shot," Youssef said.

The shooting rattled commuters who were hurried out of the station and were left standing on the sidewalk.

"It's a big knife – he can hurt anybody right? That's why they took action," said Lovreet Kaur, who heard the gunshot.

"Anything can happen right? You can't predict it."

Yellow police tape was strung up around the station and there was a heavy police presence following the incident. A large knife could be seen on the ground just outside of the entrance.

The shooting impacted SkyTrain operations on a morning already fraught with slowdowns. The station was closed and trains were not stopping on the platform.

Anyone who witnessed the shooting is asked to call the IIO at 1-855-446-8477.

Police involved shooting at 29 avenue station. Man with machete shot by police. VPD were assisting transit police when it happened pic.twitter.com/zxKyNJSEf3 — Sheila Scott (@Sheila_Scott) December 19, 2016

A few cheers as #skytrain announcement reports 29th Ave Station now open, train can continue on to downtown #Vancouver @CTVVancouver — Maria Weisgarber (@ctv_mariaw) December 19, 2016