National security affairs adviser John M. Poindexter charged last night that Congress has made it more difficult for President Reagan to cooperate with allies and friends around the globe by rejecting the sale of missiles to Saudi Arabia and aid to the Nicaraguan rebels.

In his first major speech since he succeeded Robert C. McFarlane, Poindexter said the United States remains committed to the concept of "collective security" but asserted that Congress is pushing the nation toward a policy of unilateralism or "going it alone."

In remarks prepared for the Indianapolis Chamber of Commerce, Poindexter noted that the Iran-Iraq war is intensifying on the "doorstep" of Saudi Arabia.

"So when the Congress acts to weaken our close cooperation with Saudi Arabia, which every president since FDR has strongly supported, I believe that the members of the House and Senate ought to ask themselves some hard questions," he said. Both houses have overwhemingly rejected Reagan's proposed $354 million aid package for Saudi Arabia, and Reagan is waging a final push to save the proposal.

"Who is promoting a sound policy of collective security?" Poindexter asked. "Who is making it harder for the United States to contribute to the peace of the Middle East and Persian Gulf? Who, in short, are the real 'global unilateralists'?"

Some members of Congress, however, have said the overwhelming rejection of Reagan's proposal was due in part to his failure to make a case for it before the vote.

"Congress has also tried to push us further toward unilateralism in refusing to provide aid to the brave Nicaraguans who are fighting Soviet- and Cuban-backed communism in Central America," he said. "When it refuses to apply the best means we have to pressure the communist government in Managua to negotiate, Congress ensures that no negotiated solution can be achieved which would meet the concerns of Nicaragua's neighbors and of the United States.

"That makes it more likely," he said, "that sometime in the future the United States will have to act by itself -- under far less favorable circumstances and at a far higher cost."

Poindexter also said "those who take a meat ax to our security assistance budget are making it far harder for us to meet common dangers through cooperation."