PORT AU-PRINCE, Haiti, March 9— Pope John Paul II flew here today at the end of his eight-day tour of Central America and the Caribbean and condemned what he described as the excessive inequality and misery, hunger and fear suffered by many people in Haiti.

He also demanded liberty for the Roman Catholic Church to carry out social change. His remarks came at a mass at the airport attended by tens of thousands of Haitians and leaders of the Government, headed by President-for-Life Jean-Claude Duvalier, who has ruled the country for 13 years.

The Pope was interrupted by enthusiastic shouts and drumbeats as he said of the situation in Haiti, ''There is a legitimate desire in the media and in politics for free expression.'' Addressing ''all those who have power, wealth, culture,'' he said they should ''understand their serious and urgent responsibility with respect to their brothers and sisters.''

Apparently speaking of the tens of thousands of Haitians who have fled to the United States, the Pope said that as the first nation to proclaim its independence in Latin America, Haiti ''is called up, in a special way, to develop'' so that its people ''may work without constraint, without having to seek elsewhere - and often in pitiful conditions - what they ought to find at home.''

Although he has stressed the need for social change and respect for human rights in every country he has visited, he seemed to make his message more explicit in this poorest and most crowded nation of the hemisphere. His tour, which began March 2, included visits to Costa Rica, Nicaragua, Panama, El Salvador, Honduras, Guatemala and Belize. An Arduous Day

His schedule on this final day of his journey seemed to be the most arduous. The 62-year-old Pope rose at 4 A.M. in Guatemala, flew to Belize, flew back to Guatemala two hours later and then to Port-au-Prince for a visit of several hours. (The Pope later took off for Rome on an overnight flight, the Associated Press reported.)

Although Haiti shares many of the political and social problems of the region he visited, its black and French culture is vastly different from the Hispanic and Indian traditions of Central America.

Voodoo, the African spiritism brought here by the West African slaves from whom most Haitians descend, is as much a part of the people's religious beliefs as Catholicism, and while there are 440 Roman Catholic priests, there are believed to be 60,000 houngans, or voodoo priests. Many were said to be at the mass celebrated by the Pope.

Speaking of voodoo practices, the Pope told the airport crowd not to submit to ''certain syncretic practices inspired by fear and anguish before forces that one does not understand.''

Later, at the opening of a weeklong Latin American Bishops Conference, the Pope made his first explicit statement of the trip on his concern about the dramatic growth of Protestant denominations in Latin America. He said, ''The advance of religious groups which at times are lacking the true message of the Gospel and with methods that do not respect real religious liberty, pose serious obstacles to the mission of the Catholic Church and to other Christian confessions.'' ---- Two-Hour Visit to Belize Special to the New York Times

BELIZE, March 9 - During a two-hour visit to this former British colony, where 60 percent of the people are Catholics and 40 percent Protestants, Pope John Paul called for the ''restoration of unity among all Christians.''

He said achieving such unity was ''one of the first and major tasks'' of his pontificate. Division among Christians, he said, is a ''tragedy and scandal.''

The Pope celebrated mass at an outdoor altar at the airport. A government spokesman, Norris H. Hall, estimated the crowd at 25,000, but police officers said they doubted that it was that large. All agreed, however, that it was the largest gathering in the history of this nation of about 150,000 people.