TWO YEARS AGO, under the guise of restoring prayer to the public schools, the Senate passed a bill that would have radically altered the existing system of government. The bill purported to bar the federal courts, including the Supreme Court, from reviewing any state law that related to "voluntary prayers in the public schools." The bill died a noisy death in the House Judiciary Committee. But the proposal it embodied is back, and its supporters not only foresee enactment but think it shows Congress a way to handle the abortion question as well without amending the Constitution.

This backdoor approach is something President Reagan's new Department of Justice should give early attention to. Otherwise, the president may find on his desk some morning legislation that would, for the first time, give each state -- not the federal government -- the final word on what part of the federal Constitution means.

That may not sound like a bad idea to those who believe deeply in states rights. But it would mark a profound shift in the way the country has been governed for almost two centuries. Under the prayer proposal, for instance, a protion of the First Amendment would be turned over to each state supreme court to interpret as it saw fit. The same words could, and most likely would, mean different things in Florida and Oregon. The idea that the states are united under a single rule of law, at least so far as the Constitution is concerned, would be shattered.

Once that happened, the way would be clear for Congress to take over matters away from the federal courts. It is easy to pick through the controversial issues of recent years and find subject other than school prayer and abortion for which this arrangement could be made. The apportionment of state legislatures and the drawing of school attendance zones are examples.

It is possible, of course, that the Supreme Court would find a way to fend off such an attack on its authority and on the supremacy of federal law. But to do so, it would have to get around a century-old precedent in which it upheld the power of Congress to prevent it from hearing appeals in habeas corups cases. Congress acted then to stop the justices from deciding a case challenging the post-Civil War Reconstruction Acts.

For those who are distressed by the court's decisions involving school prayer and abortion, there is a remedy that is far less damaging in the long run than this effort to subvert the federal judiciary. It is known as the constitutional amendment. That is the framework in which these battles should be fought. The Reagan administration would do everyone a favor by making that clear to its friends on Capitol Hill.