Transit authorities in New York, northern New Jersey and Philadelphia moved closer to labor contracts yesterday that would guarantee continuation of commuter trains after federally owned Conrail abandons passenger service at midnight tonight.

The possibility of a strike now seems strongest on the Hudson, Harlem and New Haven commuter lines linking New York City with Westchester and Dutchess counties and Connecticut. Only limited service will be provided Philadelphia, but full service is scheduled in New Jersey. Agreements had already been reached to guarantee operation of commuter trains between Baltimore and Washington.

A total of 214,000 commuters ride the money-losing trains that Conrail is abandoning as part of a plan mandated by Congress, which is seeking to sell Conrail to private investors but first must make it profitable.

Substantial progress toward solving complicated transfer problems was made yesterday despite the confusion created when the National Mediation Board intervened in all three outstanding disputes late Wednesday, then withdrew yesterday.

The board, charged with "maintaining the free flow of commerce" by resolving disputes in the railroad and airline industries, ordered the parties to maintain "the status quo" while its mediators worked on the problems.

However, nobody knew what the status quo would be, because the board was set to intervene at 12:01 a.m. Saturday, when Conrail will no longer have a role in commuter operations, and three different transit authorities were still negotiating work rules, salaries and schedules with the unions.

Richard Ravitch, chairman of New York's Metropolitan Transportation Authority (MTA), which will assume control of the Hudson, Harlem and New Haven lines, called Transportation Department General Counsel John Fowler yesterday morning. "I told Fowler," Ravitch said, "there is no way we will run this railroad under the old contracts" that 17 unions had with Conrail.

Fowler met with members of the mediation board, which then sent a telegram to all interested parties stating that the board's "earlier assertion of jurisdiction is premature."

Ravitch kept negotiating, and said late yesterday that the MTA has signed contracts with two of the 17 unions and is "on the verge" of agreements with 10 others. One of the five remaining contracts, with the conductors represented by the United Transportation Union, he described as a "serious problem."

The MTA, New Jersey Transit and the Southeast Pennsylvania Transportation Authority (SEPTA) are all seeking substantial changes in Conrail work rules before hiring Conrail crews to run the trains.

A major issue is the split shift, on which an employe works both morning and evening rush hours but not during midday. That type of schedule is normal in urban transit contracts but not in railroad labor contracts.

In Philadelphia, two of 15 contracts have been negotiated between SEPTA and various unions. However, SEPTA has said it plans to trim 300 to 400 employes from those holding Conrail jobs, and negotiations are proceeding slowly.

Seven of the 12 Conrail commuter lines radiating out from downtown Philadelphia will be operated Saturday, but on a reduced schedule, SEPTA announced yesterday. "We have advised people for the first few days of the business week to treat commuter rail as a last resort," said spokesman Richard Wooten.

New Jersey Transit, which will take over trains serving Newark, Hoboken, New York and Staten Island, said yesterday it has agreements with four of 15 unions and "assurances from the other unions they will work" without contracts, said Jerome Premo, executive director.