More than 26,000 union locomotive engineers went on strike yesterday, crippling nearly all of the nation's railroads in what an industry official described as the largest rail strike since 1978.

Only a few portions of the Northeast rail corridor were spared from the walkout, which stranded passengers, slowed freight deliveries and threatened Monday morning train service for an estimated 100,000 commuters, mostly in Chicago and Boston.

The strike was called when negotiations on a new contract failed.

Representatives of both sides met separately with federal negotiators yesterday and were scheduled to meet face to face at 9 a.m. today.

The Chessie System Railroads, which operates trains to Washington from Baltimore and Martinsburg, W.Va., was closed yesterday and was expected to be closed today unless there is a settlement.

Officials estimated 2,500 riders would be affected. Washington's subway system was not affected.

Amtrak, the national railroad passenger line, was not included in the contract talks, and officials said Washington-Baltimore service would continue.

Elsewhere, many other Amtrak trains were unable to move because they use lines that were being struck. "All service south of Washington, D.C., and west of Chicago has been terminated," Amtrak spokesman Bruce Heard said.

Contract negotiations collapsed seven hours after members of the Brotherhood of Locomotive Engineers started their strike at 12:01 a.m., one minute after a 60-day "cooling off" period ordered by President Reagan ended. It quickly spread across the nation by time zone, temporarily idling an estimated 300,000 railroad workers.

The Reagan administration, which had said earlier that a prolonged strike would seriously harm the already weakened economy, quickly demanded that both sides return to the bargaining table.

A few hours later, Robert O. Harris, chairman of the National Mediation Board, said he was "confident" talks would be resumed by late last night.

Conrail, the giant, federally subsidized carrier in the Northeast and Midwest, continued operations. It signed a separate union contract earlier this year.

Amtrak said it would provide service to Philadelphia, New York and Boston from Washington and would reroute trains bound for Pittsburgh and Chicago through Philadelphia, but its line to Cincinnati has been closed.

Amtrak's Silver Star, which runs between New York and Florida, was stopped in Richmond yesterday and 200 passengers had to be bused to Washington because the next link was on strike. The passengers reboarded Amtrak trains and returned to New York City on Conrail tracks.

Amtrak officials said service will be provided for up to 70 percent of its daily riders, mostly commuters in the Northeast, with about 18,000 passengers facing no service.

Locomotive engineers union president John F. Sytsma said the major stumbling block in negotiations was the National Railway Labor Conference's demand for a no-strike clause. The conference represents the major railroads with the exception of Conrail and Amtrak.

"We are striking for the right to strike," he said. The industry demand for a "no strike" clause in the 39-month contract is similar to provisions in contracts with the other 12 rail unions.

Robert O. Harris, chairman of the Na- tional Mediation Board, however, disputed Systma's claim. Harris said the main problem was wages. The sides disagree about a rule that permits the union to negotiate additional pay increases for engineers whenever other train employes receive special payment for working with reduced train crews, Harris said.

Transportation Secretary Drew Lewis and Labor Secretary Raymond J. Donovan warned that if there were no settlement by today, the administration would ask Congress to pass emergency legislation extending the cooling off period and order an end to the walkout. President Nixon ended a two-day national rail strike by signalmen that way in 1971.

The shutdown also struck Norfolk Southern, Boston & Maine, Maine Central, Richmond, Fredericksburg & Potomac and Family Lines along the East Coast. Nationwide, these major railroads were affected: Southern Pacific, Santa Fe, Burlington Northern, and Union Pacific..

Diane Liebman, spokesman for the Association of American Railroads, said the strike was the nation's largest since 1978.