Highly radioactive wastes will have to travel only on interstate highways unless state, local and federal authorities can agree on an alternate route, the Department of Transportation announced yesterday. And the Federal government will remain first among equals in reaching that aggreement.

The final regulations controlling nuclear materials shipments made a slight bow to state and local government howls over the department's initial proposal for complete federal override of their laws in the highly controversial matter. However, the federal decision will still prevail where there are conflicts, as there are bound to be.

"The public risks in transporting these materials by highway are too low to justify the unilateral imposition by local governments of bans and other severe restrictions," the regulations concluded.

In New York City, one of more than 40 local authorities with restrictions on nuclear shipments, that could eventually mean radioactive material moving along interstate routes through Manhattan. However, the new regulations, the first ever issued, do not got into effect until Feb. 1, 1982, to allow time for intergovernment talks. Meanwhile, such shipments are banned in the city and go around it from Long Island by barge.

That route could continue under the new rules, if Connecticut agrees and federal guidelines are met. "We hope to bring New York into the route-making process," said Leon Santman, head of DOT's materials transportation bureau. "That is an area where we will probably hear some more from the bridge and tunnel authorities."

The new rules are stricter for highly radioactive matter such as spent nuclear power plant fuel than for low-level items, which include X-ray film, hospital barium and other matter and research materials. For high-level objects and wastes, beltway routes around major cities are preferred to interstates that go through them, and access to the interstate must be by the most direct route.

Carriers of low-level materials do not have to stick to interstates but may choose routes based on DOT guidelines, which require consideration of population density, rush-hour timing and highway accident rates.

All carriers of nuclear material must outline proposed travel paths to DOT within 90 days so the department can identify major routes and notify the states and local governments.

If local communities object to the proposed pathways, they must work through the state to propose alternatives, holding hearings and asking for public comment. This aspect of the rules is likely to be closely watched, because as the U.S. Conference of Mayors put it in a July letter to DOT, "states generally do what is minimally required" in consulting local governments.

The new rules, Santman said, "nudge the states toward working closely with localities without being nitpicking specific."

Fred Millar of the energy activist group Potomac Alliance, which had been pushing for more local control over shipments, criticized the new regulations as "the iron fist without the velvet glove." He said the rules are "clearly a precedent for federal domination of regulation of other hazardous materials like toxic chemicals and for eventual disposal sites for nuclear waste."

The rules will also require drivers of high-level waste carriers to be retrained every two years on emergency procedures in programs provided by their companies. They will have to carry with them emergency phone numbers for every state through which they pass.

The issue of whether shippers must notify local governments before arrival of each truckload of radioactive material has been left to the Nuclear Regulatory Commission, Santman said, because of the national security aspects of such notification.