A garbage hauler who assisted in investigations of organized-crime involvement in Long Island's garbage-collection industry was killed, along with his brother-in-law, in their company offices early this morning, the authorities said.

The police had no suspects and would not say whether the killings of Robert M. Kubecka, 40 years old, and Donald Barstow, 35, were connected to Mr. Kubecka's testimony in a number of criminal and civil investigations of the industry. The Federal Bureau of Investigation has been called in to the case, officials said.

Mr. Kubecka, a resident of Greenlawn, worked for two hauling companies: one named for himself, and one named for his father, Jerry M. Kubecka. Mr. Barstow, who lived in Stony Brook, had worked with him for several years. The two were likely to be witnesses in a pending civil case in Federal court that charges many of the Island's garbage haulers with conspiring to eliminate competition and divide the industry among themselves, Federal officials said. Known as a Rebel

The police said that shortly after 6 A.M. today, someone, possibly Mr. Kubecka, called to report a shooting at the company's offices at 41 Brightside Avenue, near this village's main commercial center. When the police arrived, they found Mr. Barstow, who had already died, and Mr. Kubecka, who died on the way to the hospital. The police said they did not know how many shots were fired; no weapon was recovered.
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Mr. Kubecka, who took over the garbage-hauling business from his father, has long been known as a rebel hauler who questioned the way the industry is run. Friends and neighbors said his battle with other haulers, and his testimony at their trials, was common knowledge in the community.

In a study for the Rand Corporation in 1987, Peter Reuter wrote that Mr. Kubecka provoked the ire of many members of the industry by refusing to go along with the industry's practice of carving up business and by his work with law-enforcement officials.

The Rand report said in the late 1970's, Mr. Kubecka's company was expelled from the industry trade group, the Private Sanitation Industry of Nassau-Suffolk, after he argued against a rate increase that the association supported. About 175 of the Island's 200 haulers belong to the trade group.

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The industry and its trade group have been the subject of a number of Federal, state and local investigations, both criminal and civil, in the last decade. In 1984 and 1985, both the New York State Organized Crime Task Force and the state Attorney General's office accused the Lucchese and Gambino crime families, the trade group and several dozen hauling company officials of conspiring to control the industry.

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Ronald Goldstock, director of the task force, said Mr. Kubecka's testimony was ''crucial in both developing the evidence and in setting it out for the jury.''
''The carting industry has been controlled for such a long time that it is very unusual for individuals to speak out against those who were doing the controlling,'' Mr. Goldstock said. Massive Racketeering Suit

Many of the haulers pleaded guilty in the criminal case, and two were convicted on state antitrust charges. In the civil case, without admitting guilt, many of the haulers agreed to pay fines and to provide free trash collection.

Earlier this summer, Andrew J. Maloney, the United States Attorney for the Eastern District of New York, filed a racketeering suit against 44 Long Island hauling companies, the haulers' trade association, the Lucchese and Gambino crime families and 64 individuals. Anne Driscoll, a spokeswoman for Mr. Maloney, said Mr. Kubecka and Mr. Barstow would likely have testified in the case.

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The suit, filed under the Federal Racketeering Influence Corrupt Organization Act, charged that the defendants had effectively eliminated competition from the private sanitiation industry on Long Island. In announcing the suit, Mr. Maloney said the industry was run as a cartel ''under which individual carting companies are allocated specific residential and commercial waste collection stops, which beome the 'property' of the carter.''

Mr. Kubecka and his father, officials said, refused to join the cartel.

Mr. Maloney said the Lucchese family and various haulers forced the Kubeckas, in the early 1980's, to turn over parts of their business and to refrain from bidding on contracts. The defendants, the suit charges, threatened that if their demands were not met, they would harm the Kubeckas.

Ms. Driscoll said that it was too early to assess how the deaths of Mr. Kubecka and Mr. Barstow would affect the case.

Down the street from Mr. Kubecka's business yesterday, people working in the automobile-repair shops and stores said it was well known that Mr. Kubecka had taken risks by standing up to organized-crime figures on Long Island.

''If you shoot your mouth off, something's bound to happen,'' said an employee of an auto-repair shop, who asked not to be identified.