Photo by James Sanna | Banker & Tradesman Staff / File

Orange Line trains returned to service through downtown Boston on Tuesday afternoon after a team of engineers concluded their tunnels are safe for use, but several Green Line stops most affected by a fatal garage collapse will remain offline.

The MBTA announced that its team of structural engineers concluded it is safe to run Orange Line trains between North Station and Back Bay, which the T suspended after a portion of the Government Center parking garage above the tunnels crumbled on Saturday.

Orange Line trains will continue to bypass Haymarket Station, but the change effective immediately once again links both ends of the subway line that transports tens of thousands of riders every day.

The T will not yet bring back Green Line service between North Station and Government Center. Officials said Tuesday that “most of the debris stemming from the partial garage collapse came down on the surface directly above the Green Line,” and inspectors continue to analyze whether it is safe to run trains through the area.

Shuttle buses will remain in place for the affected Green Line stops for the remainder of Tuesday, but starting Wednesday, officials said shuttle buses “will be discontinued because the Orange Line alternative is much faster and due to the difficulty in navigating buses through crowded streets and heavy traffic.”

The Routes 111, 426 and 450 buses will also resume using Haymarket Station now that the Orange Line stations are back online.

Authorities from the Suffolk County District Attorney’s office, the Occupational Safety and Health Administration and other agencies continue to investigate Saturday’s garage collapse, which killed construction worker Peter Monsini.