Phil Hughes’ bulging disk in his upper back could morph into an extensive and throbbing headache for the Yankees.

Hughes, the No. 4 starter, was diagnosed with a bulging disk in the C-5/6 area Tuesday when he underwent an MRI exam and was examined by a St. Petersburg, Fla., spine specialist.

The Yankees hope Hughes will miss no more than two weeks. Anti-inflammatory medication and rest are the plan now. When the medicine is complete Hughes will exercise in a pool.

While Hughes is optimistic the injury won’t deter him from being ready for the start of the season, general manager Brian Cashman and manager Joe Girardi are waiting to see what develops.

“There are no guarantees until we get through the two-week process,’’ Cashman said. “It’s a question mark until we can forget about that it ever happened.’’

Girardi battled back problems as a player and understands the delicate nature of them.

“There is concern because we are not going to see him do anything for seven to 10 days,’’ Girardi said. “Hopefully everything is OK and we get him back out doing what he is supposed to be doing. Until then there is going to be some concern.’’

Hughes, 26, suffered the injury Monday covering first base during a routine fielding drill all pitchers participate in during camp.

“It’s on the spine and radiates out toward the shoulder blades,’’ Hughes said. “I felt it grab and I didn’t want to push it too far after that.’’

Despite the problem, Hughes is confident the medication will take care of the issue.

“I feel like when I get through the anti-inflammatories, I will be confident I will be symptom free,’’ Hughes said. “The positive is that I was ahead of the game throwing the ball.’’

Girardi explained that Hughes throwing bullpen sessions before arriving in camp had him ahead of other hurlers.

“Where he was at, he could have thrown two or three innings in a game,’’ Girardi said.

If Hughes misses extended time that would open the door for Ivan Nova and David Phelps — who are competing for the fifth spot — to join the rotation. And it would be a very bad way for Hughes to start the season before he can be a free agent.

Hughes is on the verge of a big payday next winter if he can duplicate last season’s effort or improve it. Hughes was 16-13 with a 4.19 ERA in 32 games a year ago when he earned $3.2 million. He will be paid $7.15 million this season.