The Transportation Department said yesterday it wants to shift $223.6 million in transit assistance away from several cities with major transit building plans, saying the government "should not start projects it so clearly cannot afford to finish."

The money, if Congress approves the change, will be used to pay for 19 smaller projects involving transit improvements and bus systems in 14 cities this fiscal year, according to the Urban Mass Transit Administration.

Congress last year had authorized the funds for new or expanded rail projects in Los Angeles, Miami, St. Louis, San Diego and Jacksonville, Fla.

Transit agency officials said the project in Jacksonville -- a proposed 2.6-mile automated rail system -- would continue to receive money from other agency sources, but that money for projects in the four other cities would be eliminated.

"In view of the federal deficit, the administration does not believe it should start projects it so clearly cannot afford to finish, or leave holes in the ground," said Ralph Stanley, administrator of the mass transit agency.

The agency has estimated that the total federal cost of the projects in the five cities would be well over $4 billion.

They include a proposed 18-mile subway in Los Angeles, new light rail systems in St. Louis and San Diego, and extension of the current elevated rail system in Miami. The money for the five projects was approved by Congress last year and any change in how it is distributed must have congressional approval.

In recent months, Congress has shown little support for the Reagan administration's attempts to reduce or dramatically change federal transit programs.

The administration in February proposed no further money for so-called "new start" rail projects such as those being considered in the five cities involved. But the Senate Budget Committee has limited the cuts to 25 percent and the House Budget Committee favors no reduction.