President Bush yesterday vetoed legislation reauthorizing Amtrak for three years, thereby dealing a setback to Northern Virginia's long-awaited commuter rail service to the District.

Bush's veto message said his action was prompted by an amendment dealing with regulation of freight railroad acquisitions, and he did not make reference either to the amount of federal money authorized for Amtrak or to an unrelated amendment smoothing the way for the Virginia service.

Bush said the freight amendment, which would require the Interstate Commerce Commission to oversee takeovers of major railroads by non-railroad interests, was "an unwarranted regulatory roadblock to financial restructuring of the railroad industry."

Amtrak's national and Northeast Corridor Metroliner service can continue under separate appropriations legislation, but unless Congress overrides the veto, commuter rail operations from Fredericksburg, Va., and Manassas may not reach Washington's Union Station.

The House is expected to override the veto easily, but a Senate vote is expected to be extremely close. Congressional sources said Wednesday that support for the legislation was so strong that Bush might let it become law, but the White House apparently decided that the Senate could be swayed to sustain a veto.

The bill contains a provision exempting Conrail from liability in accidents, the last major hurdle for the Virginia Railway Express, which is expected to take 4,000 daily round-trip passengers off Northern Virginia's crowded roads. The effect would be the equivalent of adding another lane to Interstate 95 at rush hour.

Without a liability exemption, Conrail officials will not allow passenger trains to cross the Potomac River into the District and enter Union Station. In that case, the service would terminate at Crystal City, and the projected ridership would drop to 2,680 daily round-trip passengers.

Most of the Virginia Rail Express service is on the tracks of Norfolk Southern or the Richmond, Fredericksburg & Potomac railroads, but the final miles in the District belong to Conrail.

Transportation Secretary Samuel K. Skinner, who strongly advised Bush to veto the bill, said he had no substantive objections to the bill other than the freight amendment, and he invited proponents to begin negotiations for a new bill.

"We did not veto it because the administration is against Amtrak," Skinner said in an interview. "The president did not veto it because the administration is against the Conrail commuter exception. It was vetoed because it was an attempt by the Congress to reregulate the railroad industry."

"We are very disappointed," said Virginia Secretary of Transportation John G. Milliken. "The opportunity to provide rail transportation service in a fairly inexpensive manner was a major step forward."

Said Audrey Moore, chairman of the Fairfax County Board of Supervisors, "This is not a kinder, gentler decision for Northern Virginia's traffic-weary commuters . . . . We hope our delegation will be working to try to overcome this."

Sen. Charles S. Robb (D-Va.) said the veto is "evidence of muscle-flexing rather than the application of logic to policy-making." Rep. Stan Parris (R-Va.) said he was "deeply disappointed" and promised to work to override the veto.

Members of the Virginia delegation, which unanimously backed the legislation, said they plan to mount a campaign in the Senate to explain the ICC provision and urge their colleagues not to pull the rug out from under the commuter rail service.

Should those attempts fail, congressional sponsors will have to decide whether to resubmit the Amtrak bill minus the ICC clause or attach the commuter rail provision to another piece of legislation.

However, a House Energy and Commerce Committee source said that Chairman John D. Dingell (D-Mich.) is not ready to move forward with separate legislation now, especially with a House-Senate conference committee about to meet to iron out differences in the Clean Air bill, which will take much of his time.

Judiciary Committee Chairman Jack Brooks (D-Tex.), who also has jurisdiction over the liability issue, was described as doubtful about the provision all along and not disposed to move on it.

That situation puts the squeeze on Virginia Railway officials, who must decide in the next month or two whether to buy the extra passenger cars and locomotives needed to handle the anticipated demand for service to the District. The rail company's option to buy 10 more cars for $5.9 million -- to go with the 28 cars they have already ordered -- runs out in August, said planner Stephen T. Roberts.

Virginia Railway Express has already bought eight locomotives, at a cost of $1.08 million apiece, and needs to order two more if the service is to go into the District. When service begins in October 1991, railway officials expect to run eight daily round trips -- four between D.C. and Manassas and four between Fredericksburg and the District -- with stops at 16 stations.

The freight amendment that led to the veto grew out of a hostile takeover attempt by a consortium of investors called Japonica Brothers to acquire the Chicago & North Western Railroad. The attempt was thwarted by a consortium of C&NW management, an investment firm and the Union Pacific Railroad, but midwestern politicians were upset that the Interstate Commerce Commission refused to review the takeover effort.

The ICC, which has jurisdiction over railroad mergers and takeovers by other railroad companies, said it did not have jurisdiction over takeovers by outsiders.