Electronic maps have been recalculated, navigational charts reprinted and mariners warned. Coast Guard cutters are patrolling the area to mark the new lanes with buoys in time for Sunday's shift, which adds 10 to 20 minutes of sailing.

"This is a dramatic step based on good science that makes the whales' home safer for them," said Amy Knowlton, a research scientist at the New England Aquarium.

Boston, a busy port since the early 17th century, receives at least three cargo ships carrying containers, oil or liquid natural gas each day, the US Coast Guard said.

Currently, ships cross the Stellwagen Bank National Marine Sanctuary where humpback, minke, finback and North Atlantic right whales live from March to November.

Every year, commercial ships kill as many as three whales in the 842 square mile (2,180 sq km) sanctuary that stretches from Cape Cod to Cape Ann, turning so-called vessel strikes into the top killer for whales, according to the Stellwagen Bank National Marine Sanctuary, part of the US government's National Oceanic and Atmospheric Administration.

Two whales have been hit in the last six weeks.

Only about 400 North Atlantic right whales swim in the Atlantic ocean now, compared with roughly 10,000 in the 17th century, so even one death is statistically significant, scientists said.

Alarmed by the deaths, biologist David Wiley asked the federal government and the International Maritime Organization, a UN agency, to consider moving the shipping lanes out of the busiest section of an area that also attracts about a million whale watchers a year.

"The data were compelling and people moved pretty quickly on this," said Wiley, research coordinator at the Stellwagen Bank National Marine Sanctuary. The new lanes reduce the chance of whales being hit by vessels by up to 80 percent, he said.

Commercial vessels will still sail through Stellwagen to reach Boston, but their new route separates them from the bulk of the whales.