Transportation paralysis threatens Philadelphia and, to a lesser extent, New York and northern New Jersey Monday when the Consolidated Rail Corp. (Conrail) goes out of the business of hauling commuters.

State transportation departments and transit authorities in Maryland, Pennsylvania, New Jersey, New York and Connecticut are scrambling to complete last-minute details and negotiate contracts with as many as 17 railroad labor unions each so they can assure train rides for the 214,000 weekday commuters who depend on Conrail to get to work.

The changeover technically occurs Saturday, New Year's Day, but the first real test will come with Monday morning's rush hour, when many commuters will return to work after the holidays.

Only Maryland, which has the smallest problem and the fewest Conrail-operated trains (two from Baltimore to Washington in the morning; two back to Baltimore in the evening) has nailed down final agreements for continuing service.

Conrail employes will become Amtrak employes and will operate the trains under a five-year Amtrak contract with the Maryland Department of Transportation. The first-year cost to Maryland DOT will be $1.3 million, about half of which will be recovered in fares.

Both Conrail and Amtrak are federally owned railroads. Amtrak was created to maintain passenger service in the United States after railroads found it unprofitable. Conrail was organized in 1973 so the Northeast would have freight service after the Penn Central collapsed; the commuter lines came with the package.

Congress has been trying to rid of Conrail ever since, and this change for commuters is one of the steps in that process.

The most difficult problem is in Philadelphia, where the Southeast Pennsylvania Transportation Authority (SEPTA) wants to eliminate 300 to 400 Conrail jobs as it takes over two of the nation's storied commuter lines: the Reading and the Pennsylvania Main Line. New York, Connecticut and New Jersey authorities appear on the verge of solving their takeover problems.

The Philadelphia situation has been marked by court fights and a statement early this week by David Gunn, SEPTA's executive director, that because there were no signed contracts and SEPTA wasn't sure who was coming to work, there would be no commuter rail service until a training period of two or more weeks was concluded. That was necessary, he said, to ensure safety on the lines, which carry about 90,000 riders daily.

A local court intervened Tuesday and ordered SEPTA to provide as much service as is safely possible, and late yesterday the SEPTA board decided not to appeal that ruling. A spokesman warned, however, that service will be limited.

The central issue has been the disparity between salaries paid to SEPTA subway operators and bus drivers (about $20,000 annually) and those paid the 1,500 Conrail employes who would become SEPTA employes and who now make as much as $35,000 annually.

An emergency board set up to resolve such disputes ruled recently in favor of SEPTA's final offer, which capped salaries at $35,000 for engineers for three years. The unions have promised to work, even without contracts; Gunn has insisted that if they work without a contract, it will be under SEPTA rules and salaries, not Conrail rules.

In New York, the Metropolitan Transportation Authority (MTA), which operates the subway and bus systems and the Long Island Rail Road, is concluding negotiations with 17 rail unions so it can take over about 5,000 Conrail employes who operate the commuter trains on the Harlem, Hudson and New Haven lines. The Connecticut Department of Transportation reimburses the MTA for its operations between the state line and New Haven.

Officials of the labor unions and the MTA predicted that service would continue and that the contracts will be signed.

New Jersey commuters to Hoboken, Newark, New York and Staten Island are in a similar, but less certain, situation. New Jersey Transit, the statewide public bus authority, is also negotiating to take over Conrail service but has made elaborate plans to provide alternate bus service for about 60 percent of its Conrail commuters starting Monday if there are labor problems on the rail system.

"We're down to economic issues that I can't discuss," said Jerome Premo, executive director of New Jersey Transit. "The unions have been respectful and the next handful of days will be crucial." The unions have offered to work without contracts, Premo said, but he is anxious to have final agreements in place.

Both the MTA and New Jersey Transit are seeking substantial changes from work rules in Conrail contracts; Amtrak has already won significant changes in its contracts for the Maryland service and for its passenger operations in the Northeast Corridor between Washington and Boston.

Hauling passengers is a losing proposition for railroads throughout the Free World, and that is the reason Congress, under substantial prodding from Transportation Secretary Drew Lewis, ordered Conrail to divest itself of its passenger operations.

The order came in the Omnibus Reconciliation Act in July, 1981, and left transit authorities with little time to plan the massive takeover of more than 1,500 daily commuter trains that will occur Saturday.

When the transfer is completed, Conrail will be completely out of the passenger business and can concentrate on improving its financial performance in the freight business.

When the Reagan administration took office, Lewis said he wanted to rebuild Conrail in such a way that it would be attractive enough to sell to private business. That meant, among other things, getting rid of the commuter service, which, Conrail claims, has cost it $350 million beyond fares and federal, state and local subsidies over the last five years.

Conrail faces two major tests next year as part of the plan to sell off the railroad that was included in the reconciliation act. If Conrail is found to be profitable after the second test next October, than it is supposed to be transferred by the Transportation Department to private owners in a yet-to-be-determined manner.

Conrail is projecting a net income of $130 million this year, including $90 million from the sale of tax benefits it could not use. However, under the accounting method required of railroads by the Interstate Commerce Commission, Conrail expects to report a loss of about $35 million.