Four US tourists and an Australian pilot died after their light plane came down on a shopping centre on Tuesday.
It had just taken off from the small Essendon Airport, which reopened on Thursday. The nearby shopping centre remains closed "until further notice".
Safety officials said they would investigate with "an open mind" and make a preliminary report next month.
The victims were pilot Max Quartermain and passengers Greg Reynolds De Haven, Russell Munsch, Glenn Garland and John Washburn, four men from Austin, Texas, who were on their way to Tasmania's King Island for a golfing trip.
Greg Hood, chief commissioner of the Australian Transport Safety Bureau (ATSB), said four investigators would examine the scene for several days.
"We're very much in the gathering of evidence phase," he said.
Police said the flight appeared to have had a "catastrophic engine failure" before Mr Quartermain gave two mayday calls.
However, Mr Hood said investigators would make no assumptions.
"We'll look at maintenance records, the history of pilot, the history of aircraft… at this very early stage, we're not going to speculate in relation to any specific part of the investigation," he said.
The West Australian newspaper reported the Beechcraft B200 King Air plane recently passed a safety check.
The inspection by industry regulator Civil Aviation Safety Authority (CASA) found no issues with the plane or pilot, the newspaper said.
Mr Quartermain was investigated by the ATSB over a near mid-air collision in September 2015, but he later passed a series of proficiency tests set by CASA.
Victoria's Premier Daniel Andrews said the crash on Tuesday was state's worst in 30 years.