An extensive investigation in the Bahamas that found "suspicion and distrust on both sides" has pointed to friction between U.S. and Bahamian authorities as a major obstacle to slowing the flow of illegal drugs into the United States.

The Royal Commission of Inquiry, in its report issued last week after more than a year of probing, mainly detailed corruption in Prime Minister Lynden Pindling's government that has helped make the island nation a paradise for drug traffickers, as well as vacationers. But it also reported lack of cooperation between U.S. and Bahamian officials so acute that it has undermined efforts to halt the smuggling.

The Reagan administration organized a series of task forces three years ago to halt trafficking in drugs, particularly along the main route from Colombia to Florida. The Bahamas quickly became a concern. U.S. enforcement agents estimate that two-thirds of the cocaine entering this country passes through the chain of 700 tropical islands only a few hours' speedboat ride from the coast of Florida.

For two years, the two governments have been trying to negotiate a mutual legal assistance agreement. Administration officials point out, however, that such an agreement also would have to deal with Bahamian bank secrecy laws, regarded as a loophole for laundering drug money by the United States but cherished as a major revenue source by the Bahamas.

Against that background, each government has accused the other of stalling on the agreement.

Attorney General Paul Adderly of the Bahamas told the commission that several initiatives were largely ignored by the Reagan administration. The commission, apparently accepting this view, accused the United States of rejecting proposals that "could have avoided subsequent events that have brought this commission into being and that have soured U.S.-Bahamas relations."

"We have concluded that failure to respond positively and unequivocally . . . represent s serious neglect and unwarranted indifference on the part of U.S. authorities," the commission declared.

A Washington-based administration official involved in the exchanges countered that, instead, the Pindling government repeatedly refused to pursue the negotiations.

"One thing after another," he added. "It just kept being postponed, postponed and postponed."

A spokesman for U.S. Ambassador Lev E. Dobriansky in the Bahamas declined to explain the delay, but said: "We look forward to institutionalizing cooperation between our two governments on judicial matters and matters of law enforcement, including drug interdiction and exchange of information on narcodollars by means of a mutual legal assistance agreement."

Despite the dispute over cooperation, U.S. and Bahamian officials concluded 10 years of negotiations last April with a $100 million agreement for renewing leases on three U.S. military facilities in Bahamian islands. These included an Air Force missile-tracking post on Grand Bahama Island, a Coast Guard radar station on San Salvador Island and the Navy's Atlantic Underwater Testing and Evaluation Center, which reportedly has equipment to track Soviet submarines.

Besides delays in the legal agreement, the commission said Bahamian feelings were rankled by disputes with a U.S. diplomat stationed in Nassau, the capital, and U.S. undercover drug operations that it said were mounted on Bahamian soil without consent.

The diplomat, Andrew Antippas, was charge d'affaires until Dobriansky's appointment last year and now is a consul in Seoul. Bahamian and U.S. officials said the Pindling government told him to leave in the summer of 1983; he departed at the end of what U.S. officials said was a normal two-year tour.

A Bahamian official said Antippas was asked to leave because of dissatisfaction with his attitude toward government figures and contacts with opposition figures "far beyond the boundaries of diplomacy." Pindling and Adderly "apportioned a considerable amount of responsibility" on Antippas for the "fairly low level" of relations, the commission found.

In addition, the commission explored Bahamian resentment at what it said were U.S. operations carried out without adequate coordination. These included what the commission said was a U.S. attempt in 1979 to entrap the former minister of youth, sports and community affairs, Kendal Nottage.

"There is no dispute over the fact that these U.S. agencies' illegalities occurred at a time when there was a full cooperative atmosphere in existence in the Bahamas," the report added. "Such attitudes cannot facilitate good relationships."

A National Broadcasting Co. report in September 1983 that revealed the Nottage operation prompted Pindling to name the high-level commission. The panel instead found evidence of extensive drug-related corruption in the government. It also said that information broadcast by NBC was leaked by U.S. drug enforcement agents to incriminate the Pindling government.