Federal Aviation Administrator J. Lynn Helms is standing in the way of the Boeing Corporation's hopes of using a version of its new, two-engine 767 jetliner for transoceanic flight.

Helms said recently that he is "not persuaded that a two-engine airplane provides the safety and reliability I seek" for transoceanic operations.

Helms comments came in a speech last Friday to institutional investors. As he was speaking, Boeing was making final arrangements for a press conference here today to announce the stretch version of the 767. According to aviation sources, Boeing hopes to certify that version for transoceanic service, which would require Helms' approval.

Current Federal Air Regulations require that a jet-powered airplane carrying passengers have at least three engines if it is going to fly "over a route that contains a point farther than one hour flying time from an adequate airport." That is to assure that adequate power remains for safe landing if one engine fails or has to be shut down.

The jets used in transoceanic flights include two four-engine pioneers, the Boeing 707 and the McDonnell Douglas DC8, and the newer jumbos: the Boeing 747, with four engines, and the McDonnell Douglas DC10 and the Lockheed L1011, both with three engines. The 767 is the newest Boeing jumbo.

Boeing spokesman James Boynton, asked about Helms' speech, said, "We will just keep working diligently toward" winning approval. In the meantime, he said, "there is an awful lot of area to cover that is not encumbered by an ocean."

Boeing has sold 175 of the 767s for between $46 million and $52 million each. The plane has a range of 3,200 miles in its present configuration and can carry between 211 and 290 people, depending on how the seats are arranged. A stretch version apparently would have sufficient additional range to qualify it for trans-oceanic service.

Helms also said that he intends to continue some air traffic control restrictions at the nation's busiest airports even after the control system returns to normal following the strike and subsequent firing of 11,400 controllers in 1981.

Normalcy, Helms said, will be "largely accomplished by the end of this year," but that "we'll still have to use some sort of flow management." None of the many new controllers working for FAA, Helms said, "will have seen six to 10 aircraft holding in a stack. Their entire experience has been based on no delays at arrival."

Without flow control, he said, a combination of normal traffic and heavy thunderstorms could create as many as 68 planes in a holding pattern over New York City. "I simply can't take that risk," he said. "I want our controllers to ease into it, to see two in hold for a couple of months, then three or four . . . . "