Tommy Haynes captured both horizontal jumps in the 89th National AAU indoor track and field championships today but, as usual, there was more excitement off the track than on it.

The AAU refused to accept late entries from high jumpers Ed Fern and Mel Embree, prompting the entire men's field to threaten a boycott of the event.

The deadline for entries was Feb. 15, the day Fern and Embree sought to enter the meet by phone. They were told they would be mailed entry blanks, but the pair claimed the forms never arrived. When they came to New York, they were denied entry by a vote of the games committee.

After the boycott plans became known, the games committee met again, on the Madison Square Garden infield, during the meet and affirmed its earlier decision.

"The games committee turned down the appeal," said meet director Ollan Cassell, also the executive director of the AAU. "If we permitted them to compete, we would have to pick up a number of other athletes who did not enter properly. I don't think the games committee can determine the situation on the basis of athletes refusing to jump."

At the appointed time, the athletes met in the infield, then most walked away. Only Gene White, Paul Underwood and Glenn Irion elected to compete.

"I qualified for the meet, I'm a high jumper and I busted my butt getting here, so I'm going to jump," White said.

Haynes won the triple jump for the third straight year with an effort of 55 feet 2 inches. As soon as he completed his final try, the pit was turned over to the long-jumped, and Haynes won again, leaping 26 feet inch.

"This was my first competition this year," said Haynes, an assistant coach at West Point, "I've really just been coaching. If I have time, I take a few bounds with the team. I don't have my technique down, but I'm real strong. I was powering my way. It only takes one punch in the long jump, but I surprised myself in the triple."

Haynes was fifth in the Olympic triple jump. He hope to compete in both events at Moscow in 1980 and will try both in the U.S.-Soviet-Canada meet in Toronto March 3-4. The top performers in today's meet are eligible for the U.S. team.

Arnie Robinson, the Olympic championship in the long jump, suffered a bruised heel on his first try today, limping from the epit.

George Frenn took the 35-pound weight throw, held at Princeton's Jadwin Gym. It was his sixth AAU title but he was almost overshadowed by seven-time winner Bob Backus who three 62 1/2 for sixth place at the age of 50.

Kathy McMillan, the Olympic silver medals, set a meet record of 21-4 1/4 in the women's long jump, topping retired Martha Watson's 1975 mark by 2 inches.

Sue Brodock won the mile walk for the fourth straight year and, as usual, established an American record, 7:05.9.

Joni Huntley took the high jump from Pam Spencer on fewer misses as each cleared 6 feet. Paula Girven, the Olympian from Woodbridge, Va., was troubled by a sore tendon and cleared only 5-10 for third place.

Howard advanced to the finals of both the sprint-medley and mile relays. The D.C. Strides won their heats in both events, but were too slow to qualify for the sprint-medley final.