The Governing Board of the National Council of Churches took a strong stand this week against legislation that would put issues such as abortion and school prayer outside the jurisdiction of the federal courts.

A resolution adopted by the board at its semiannual meeting in New York put the council on record against any legislation "that would weaken the access of any citizens to the federal courts for vindication of their rights under the Constitution of the United States."

In recent years, legislation has been proposed that would bar the federal courts from ruling on cases involving prayer in public schools and abortion.

While such measures have been promoted as a restoration of states' rights, the NCC document noted, "the motivation behind them is to reverse recent rulings of the Supreme Court that are objectionable to some people."

Another resolution opposed as "unworkable" President Reagan's call for a constitutional amendment requiring a balanced budget.

While calling the goal of a balanced budget "sometimes desirable," the NCC resolution cited "widespread concurrence among a broad range of the nation's economists" that such legislation "could actually be harmful and even dangerous to the nation's well-being, since it would rob Congress and the president of the flexibility they need to respond effectively and quickly in times of crisis."

In the current economic recession, the resolution continued, funding for social programs designed to help the poor has been cut sharply. "If the government were under a mandate to balance the federal budget now, such balancing, of necessity, would be done at least in part at the expense of the already diminished programs which serve needy people."

A resolution on Central America expressed concern over reports that the United States "is supporting covert activities to destabilize the Nicaraguan government" and said that stepped-up U.S. military aid to Honduras has contributed to increased danger of war between Honduras and Nicaragua.

The resolution "protests strongly U.S. involvement in activities designed to destabilize the government of Nicaragua, including the funding of opponents" of the Nicaraguan regime. It encourged U.S. cooperation with other Latin American nations in pursuit of "negotiated solutions" to Nicaraguan-Honduran tensions.

The National Council of Churches provides an interdenominational structure through which its 32 Protestant and Eastern Orthodox member denominations cooperate in a variety of activities. Positions taken by the Governing Board, made up of representatives of member bodies, are considered advisory, not binding.

Board members strengthened the NCC's ties to the National Anti-Klan Network, an Atlanta-based movement composed of 52 civil and human rights, labor, religious and community organizations, and urged NCC member denominations to join.