Defense Secretary Casper W. Weinberger, in his first big rebuff to the Joint Chiefs of Staff, will recommend to President Reagan that the United States establish a new and separate military command for Perisan Gulf emergencies, government officials said last night.

Weinberger and his deputy, Frank Carlucci, were putting the finishing touches on their detailed recommendation yesterday, with hopes of having it in Reagan's hands no later than today.

Weinberger met with the four members of the Joint Chiefs in a long, secret session at the Pentagon last Friday to explain to them why their recommendations were being rejected.

"There were a lot of long faces down there," said one Pentagon official in relating the reactions of the chiefs.

Chairman David C. Jones of the Joint Chiifs; Gen. E. C. Meyer, Army chief of staff, and Adm. Thomas B. Hayward chief of naval operations, all favored putting the present day Rapid Deployment Force under the U.S. European Command headquartered near Stuttgart, Germany.

Commandant Robert H. Barrow of the Marine Corps, the fourth member of the Joint Chiefs, recommended that the RFD become an arm of the Pacific Command located in Honolulu, arguing that "the now force" for responding to Persian Gulf emergencies consisted largely of Marines and Navy warships.

Weinberger, sources said, argued that adding an appendage to either of those commands would not correct the confused lines of authority that have subjected the Rapid Deployment Force to so much criticism in Congress and elsewhere. Sen. William S. Cohen (R-Maine), chairman of the Senate Armed Services subcommittee which has been probing the RDF command structure, has been at the forefront of those demanding reform beyond a new home for the outfit.

The Pentagon recommendation going to Reagan addresses that problem by calling for a theater commander who would control the forces in clearly marked off territory around the Persian Gulf, land as well as sea.

Under the present setup, the European Command controls the land and the Pacific Command the waterways in some of the key areas of the Persian Gulf.

Although no chief got his way, they are expected to close ranks behind the separate Persian Gulf command setup because if is far preferable to the current structure of the RDF. As it is now constituted, the RDF serves as a small planning staff in peacetime for the Readness Command at MacDill Air Force Base in Tampa. But in a Persian Gulf war, the commander of the RDF would suddenly become the field general for operations in the theater. The Weinberger plan would change this.

The confusion on the ground during the ill-fated multi-service attempt to rescue American hostages in Iran last April gave impetus for straightening out the lines of authority of the RDF.

Some military leaders outside of the Joint Chiefs pressed not only for establishing the kind of separate theater command for the Persian Gulf that Weinberger has chosen, but recommended it be located in that area as well to send a signal of determination to the Soviets.

Sources said Weinberger and Carlucci are keeping this option open for the future but feel it would be premature to take the step today.

For one thing, it is not certain any Persian Gulf nation would allow even a small-sized U.S. military staff, like the 261 who comprise the RDF headquarters at MacDill, on their territory. For another, sources said, Weinberger and Carlucci want to refine the Persain Gulf command sturcture before deciding on where to locate it.

An interim possibility is to use a ship as an interim headquarters for the Persian Gulf staff. Plans for the new theater command have not been refined to the point where such a decision can be made, source said.

If Reagan does the expected and establishes a separate new military command for Persian Gulf emergencies, Marine Lt. Gen. P.X. Kelley, the first and current RDF commander, has the inside track on running it. This would probably mean a fourth star for him to make him equal in rank to other theater commanders.

President Carter established the Rapid Deployment Force in an attempt to signal that the United States stood ready to use military force to protect oil supplies in the Middle East. However, the RDF is a paper outfit in the sense that it has no soldiers of its own but would rely on existing forces, with the 82nd Airborne Division one of the outfits on call for Persian Gulf duty.