NASSAU, Bahamas (AP) _ Prime Minister Lynden Pindling's governing party beat back its strongest challenge in his 20 years in power, winning re-election by a wide margin despite opposition charges of complicity in the drug trade.

In incomplete, unofficial returns early today, Pindling's Progressive Liberal Party had won at least 29 of 49 seats in the House of Assembly, surprising political analysts who had expected a close parliamentary election.

The opposition Free National Movement led by Nassau lawyer Kendal Isaacs took at least 13 seats. Isaacs won his seat handily.

Neither Pindling, who won a sixth term in office, nor Isaacs had any immediate public statement.

Pindling, 57, who became the nation's first black prime minister in 1967 and was instrumental in the movement that gained the Bahamas independence from Britain in 1973, spent election day Friday at his constituency of Kemp's Bay on Andros Island.

Deputy Prime Minister Clement Maynard claimed victory for the party about three hours after the polls closed.

The victory meant ''the Bahamian people are not going to support a party that is even more corrupt and more involved in drugs than anyone in the PLP,'' Maynard said.

Maynard, who is also foreign minister and tourism minister, said he ''had no doubt that American agencies have interfered in the Bahamian elections.'' He would not identify those agencies and said their action had nothing to do with official U.S. policy.

The government has been accused by the U.S. Congress of not doing enough to curb drug smuggling. The U.S. State Department estimates 40 percent of the cocaine and much of the marijuana entering the United States comes through these islands off Florida.

Hubert Ingraham and Perry Christie, former Cabinet ministers fired by Pindling in 1984 for accusing him of failing to act forcefully against officials implicated in a drug scandal, became the first independents in two decades to win seats.

Another one-time Pindling associate-turned-antagonist, former Deputy Prime Minister Arthur Hanna, was unopposed for a parliamentary seat. As a PLP member, however, he was counted among the preliminary total of 29 PLP seats.

Three races were too close to call early today, and voting was suspended in two outer-island races because not enough ballots were available at several polling places, officials said. Voters unable to cast ballots were told they could do so today.

Other minor election problems were reported, including polling places opening late, voters not knowing their polling locations and ballots not arriving on time. But observers reported no indication of fraud or a pattern of irregularities favoring one side over the other.

A turnout of 90 percent of the 99,000 registered voters in the Bahamas was predicted. Voters in this nation of 700 islands were ferried to polling places in boats, small planes, helicopters and cars.

The corruption issue was first raised in a 1984 report by an independent Commission of Inquiry, and opposition to the prime minister mounted after he refusd to answer questions raised about his personal finances.

The commission reported he had spent $4 million, or eight times his government income, from 1977 to 1983. It questioned a series of gifts, contributions and unsecured loans and said he couldn't acccount for $180,000 in his bank accounts.

The panel also linked two of his Cabinet ministers and some of his cronies to drug trafficking. The two ministers, Kendal Nottage and George Smith, resigned but remained loyal PLP members and were elected to the House of Assembly on Friday.

A subcommittee of the U.S. Senate Foreign Relations Committee, concerned about a joint Bahamian-U.S. program to intercept drug smugglers, sent a three- man crew of election observers.

Maynard said ''a lot of nonsense is coming out of Washington.''

The Bahamas is ''doing all that we can'' to cooperate with the United States in intercepting drug runners, he added. ''But you are giving us hell in the meantime. ... We cooperate and you still want more. What do you want from us?''

Some ''meddlers'' considered it ''advantageous for the FNM to win the election,'' Maynard said. ''If that isn't interference, what the hell is it?'' he shouted at a news conference.

U.S. Embassy officials said American investment in the Bahamas amounts to $3.5 billion, including hotels, real estate and other business interests.

This country is the top foreign destination for American tourists, and 75 percent of its $800 million worth of imports were from the U.S. last year. Forty-five percent of its $245 million in exports went to the U.S.