Both crewmen were killed when an Air Force F-4D Phantom jet on a training mission crashed Tuesday in the Straits of Florida, an Air Force spokesman said. The victims' names were not released.

A New Jersey Air National Guard jet fighter crashed in a remote section of the Pine Barrens in Burlington County yesterday, starting a fire that scorched at least 90 acres of woodland. The two fliers aboard ejected safely before the crash and were reported to have sustained minor injuries.

The plane, an F-4E Phantom of the Guard's 108th Tactical Fighter Wing, went down in a heavily wooded area southeast of Chatsworth, N.J., at 4 P.M. while on a training mission from McGuire Air Force Base, 20 miles to the north. It exploded upon impact in a region of scrub pine, part of the preserve that covers one million acres in southern New Jersey.

The resulting fire was brought under control in about two hours.

The pilot, First Lieut. Benjamin J. Zerbey, 29 years old, of Florence, and the flight systems operator, First Lieut. Michael L. Cunniff, 29, of Cedar Grove, were rescued by a state police helicopter and taken to Walson Hospital at Fort Dix. Lieutenant Cunniff was reported to have sustained a shoulder separation and possible broken arm. The hospital said both men were being held for observation.

LEAD: Two military reconnaissance jets collided and crashed in flames in a remote area today, killing two crew members while two others parachuted to safety, the authorities said.

Two military reconnaissance jets collided and crashed in flames in a remote area today, killing two crew members while two others parachuted to safety, the authorities said.

One crew member's body was found after the crash of the RF-4C Phantom II about 4 P.M. near Lake Brownwood, Texas Ranger Norman Autrey said. Debris from the aircraft was spread over a two-mile radius, he said.

Fire Capt. Donald Reiger said officers found smoldering airplane parts and human remains in a field just west of Texas Highway 279, a half-mile from Lake Brownwood.

Witnesses said they saw three parachutes, one empty, falling to the ground after the crash, said Steve Wittenberg, a dispatcher for the Department of Public Safety.

Ranger Autrey said a witness told him he saw the planes overhead, and that as they passed one was flying right side up and the other was inverted.

Captain Reiger said investigators were told the pilots were practicing a dogfight. Airman Sean Ruark, a spokesman at Bergstrom, said she could neither confirm nor deny that report.

The RF4C Phantom II reconnaisance planes were from Bergstrom Air Force Base.

One crewman, Richard Dietrich, 28 years old, of Austin, was in good condition at Brownwood Regional Hospital with second-degree burns and leg bruises, the hospital's director of public relations said. Another crew member, James Johnston, was not treated.

INDEPENDENCE, Mo., Jan. 21 (AP) - One of those presumed killed in the collision of a private plane and a military aircraft Tuesday was Brig. Gen. David H. Stem, deputy commandant general at Fort McClellan, Ala., and commandant of the military police school there, the Army said today in Washington.

The collision occurred over one of the Army's largest munitions plants, killing five other people on the planes, the authorities said.

An Army spokesman, Maj. Bill Auer, identified the dead pilot of the military aircraft as Maj. Michael G. Johnston of Alexandria, Ala.

The National Transportation Safety Board has begun a special inquiry into hazardous incidents involving control of planes at the nation's airports.

The agency's longtime concern over the problem was rekindled by an incident in Minneapolis March 31 in which a DC-10 jumbo jet that was taking off flew just 50 feet above another DC-10 that had been cleared to taxi across the takeoff runway.

This was followed by numerous other incidents, including a nighttime accident in Birmingham, Ala., June 20 in which the pilot of a small cargo plane awaiting clearance for takeoff was killed. His plane was struck by a National Guard F-4 Phantom jet that had been given permission to land on the runway where the cargo plane was.

The safety board is looking for recurring reasons for traffic mistakes at airports - those due to controllers, pilots or difficulties in communication between the two. Its goal is to establish the extent to which the breakdowns are due to simple human forgetfulness, overwork, distractions or inadequacies in training or procedures. And the board aims to come up with recommendations for reducing the hazard.

Last week the head of the Federal Aviation Administration, which operates the air traffic system, made conference telephone calls to personnel at more than 400 airport towers to give his views on the problem and announce some corrective measures of his own.

'Surface Error Incidents'

The F.A.A. Administrator, Donald D. Engen, disclosed that despite previous preventive efforts the number of airport traffic conflicts was increasing. Through July 5, he said, there were 54 ''surface error incidents,'' compared with 41 for the same period in 1984.

Mr. Engen announced two initiatives to cope with the hazard and said there would be other follow-up actions.

The immediate step is aimed at improving coordination between the two tower controllers usually responsible for aircraft movements on particular runways. The ''local'' controller has the job of radioing permission to pilots to land or take off on what is known as the ''active'' runway. The ''ground'' controller radios instructions for taxiing to and from runways, or across them.

In busy periods, Mr. Engen said, a third person, perhaps a supervisor, should be present to help the two controllers dovetail their moves ''and to provide an extra set of eyes.''

''He or she,'' the F.A.A. chief said, ''should insure that proper vigilance, particularly the scanning of runways, and coordination is taking place.'' He noted that of the 54 incidents this year, ''30 involved some sort of breakdown in the ground and local control position coordination procedures.''

Emphasis on Standardization

In the Minneapolis incident involving the DC-10's, the controllers, standing alongside one another, apparently got their signals crossed on how many planes would be allowed to taxi across the active runway before further takeoffs were permitted. A third ''coordinator'' might have detected the conflict in time to avert the near-collision.

The second action announced by Mr. Engen was the acceleration of a program to standardize the procedures by which those two control positions would be operated.

Other follow-up actions that officials say are under consideration include limiting points at which planes may taxi across active runways, developing ''memory aids'' to help local controllers remember when planes or ground vehicles, such as snow plows, have been given permission to move onto active runways, and equipping the controllers' training school with a tower cab where operations for specific airports could be simulated.

The safety board's special inquiry is expected to be completed in about three months. Such investigations are undertaken occasionally when the board detects a possible pattern in accidents. Normally it concentrates on individual crash investigations.

Among the special inquiries conducted in recent years were studies of commuter airline safety, the overall traffic-control system, the ability of aircraft to tolerate crash forces and the safety standards for airport design.

The study of the on-the-airport traffic problem is to be directed by Jack Drake. Mr. Drake said in an interview Friday that the survey might cover more than the eight incidents this year on which individual investigations had been started. In addition to the near-collision at Minneapolis and the fatal Birmingham accident, they included a second Minneapolis incident and others in Philadelphia, Austin, Tex., Midway Airport in Chicago, Boston, and West Palm Beach, Fla.

Two United States marines ejected from their F-4 Phantom jet fighter and were rescued from their rubber raft early today in the Pacific Ocean 65 miles southeast of Okinawa, a Marine Corps spokesman said. They were not identified and the cause of the crash is being investigated. They were on a training mission from Kadena Air Base on Okinawa.