Secretary General Amr Musa said the Security Council should stick to its task of maintaining peace, especially in Iraq and the occupied Palestinian territories.
"The Security Council should deal with the principal matters related to its competence - monitoring and preserving international peace and security," he said in Cairo on Wednesday.
"There are crises in the Middle East which we believe the Security Council has not dealt with, such as what is happening in the occupied territories and Iraq," he said.
"These discrepancies and double standards have led and are leading to big question marks about the Security Council and its role," he added, after talks with visiting Lebanese Prime Minister Rafiq Hariri.
Arab governments have criticised the UN resolution on Lebanon last Thursday as unjustified interference in Lebanese affairs.
Without mentioning Syria by name, the resolution called for the withdrawal of foreign forces from Lebanon and for presidential elections without foreign interference.
Syria dominates Lebanon politically and has some 17,000 soldiers in the country. It first sent the troops there during the 1975-1990 civil war.