AMTRAKS EXISTING SYSTEM of passenger trains has received a brief reprieve from a House-Senate conference committee. The conferees have agreed to provide funds through the next fiscal year for all the trains now running. But some provisions of bill suggest that it will be the last year of a nationwide network. The annual deficit of those trains - about $600 million - seems to be larger than Congress is willing to underwrite on a permanent basis.

Two provisions in the conference report indicate the way the wind is blowing. One directs the General Accounting Office to report by Dec. 31 on how Amtrak's fare structure has affected intercity buses; the other authorizes the Interstate Commerce Commission to hold hearings on whether those fares are unfair to the bus industry. Both are the result of a strong lobbying effort earlier this yer by the bus companies. So is the language in the conference report that says, "The conferees strongly feel that Amtrak fares must be altered to reflect, more appropriately, the true cost of providing passenger service."

Amtrak is caught in a classic squeeze. It has been able to increase the number of riders on some rotes by cutting ticket prices drastically. Even with that increase, however, the routes haven't reached the break-even point. If the fares are raised in an effort to do what Congress wants done, the odds are that the number of passengers will decrease and the deficits will get even bigger. If they aren't raised, the railroad's critics will continue to complain.

The GAO study, in particular, may be crucial to Amtrak's future. If it shows that Amtrak is cutting into the intercity-bus companies will have made their point. They argue, with some validity, that the government should not be underwriting a fare structure that diverts business from them, especially since most of them operate on a slim profit margin. If, no the other hand, the GAO study shows that Amtrak's fares are diverting people who would otherwise travel by automobile, the case for a continuation of its present policies will be much stronger.

Either way, Amtrak's network of trains is likely to shrink in the fall of 1979. Some of its routes show no potential of ever breaking even, regardless of ticket prices. Those are almost certain to be abandoned under the procedures established in the bill. It directs the secretary of transportation to produce final recommendations for a new route structure by the end of December and orders that those recommendations go into effect during fiscal 1980 unless disapproved by either house of Congress. Secretary Brock Adams has already designated some routes as candidates for elimination. The political pressure that has kept several of those in operation this long - or created them in the first place - seems diminished by the thrust of this new legislation, which is clearly aimed at producing a smaller and less costly Amtrak.