The agency said it handled more than 538,000 tons of autos during the first half of the year, compared with 413,403 tons for New York — last year's market leader — during the same period.
Helen Delich Bentley, the former congresswoman for whom the port is named, hailed the results.
"We have been running a very close second for a long time, and it is with much joy that we have jumped over New York," said Bentley, now a consultant to the maritime industry.
The port agency said the data were compiled by the U.S. Census Bureau and analyzed by Global Trade Atlas.
While Maryland Gov. Martin O'Malley hailed the results as "another good step forward in continuing to rebound from one of our country's most challenging economic periods," it is unclear whether Baltimore — previously the No. 2 port for autos — can hold the No. 1 spot for long.
Scher said the world auto market was heavily affected by this spring's earthquake and tsunami in Japan. He said New York and Jacksonville, Fla., the No. 3 automobile port, are highly dependent on imports from Japan.
Baltimore, by contrast, does a strong business in exports by American producers — especially Chrysler — and in imports by German manufacturer Mercedes-Benz.
"It's obviously a very good sign to lead off the year, but keep in mind that Japanese effect," Scher said.
The port spokesman also noted that exports of American autos through Baltimore were up 38 percent during the first half, compared with a 25 percent increase for New York.
Scher said Baltimore's port has helped boost its auto business by instituting a "white-glove treatment" program, under which it holds regular meetings with members of the auto supply chain with the aim of improving performance.
According to the port administration, about 270,700 cars crossed Baltimore's docks from January through June, up 30,000 vehicles from last year. Overall cargo shipments increased 13 percent, to 4.5 million tons, during the six-month period, the agency said.
If the port can hold the lead in cars, the auto trade would join roll-on/roll-off equipment — agriculture and construction vehicles — as well as trucks and imports of gypsum, forest products, sugar, salt and iron, all categories in which Baltimore leads the industry.
The port administration estimates that the auto trade through Baltimore generates 1,150 jobs in the region.