For the second time in as many years Alpine Eagle will be missing from the Melbourne spring carnival.

His devastated trainer Tony McEvoyi says the horse has a throat issue and will undergo surgery to fix a soft palate problem.

Alpine Eagle missed most of last year's spring carnival after being diagnosed with a cracked pedal bone after two starts.

McEvoy sent Alpine Eagle to the University of Adelaide's Roseworthy campus to have the entire checked over following his last-start eighth behind Raw Impulse in the Tokyo City Cup at Morphettville on September 17.

"He's displacing his palate frequently and not getting any oxygen," McEvoy said.

McEvoy believes Alpine Eagle has stopped trying in his races and hopes the surgery will rectify the situation.

After a promising first-up sixth behind Black Heart Bart at Flemington, Alpine Eagle finished 11th in the Makybe Diva Stakes won by Palentiono at Flemington on September 10.

He backed up a week later with his disappointing effort behind Raw Impulse.

McEvoy said it was not coltish behaviour that had stopped Alpine Eagle performing at his best.

"I know he was colty in the mounting yard at Flemington but normally he's fine," McEvoy said.

"We'll get a little procedure done on him and turn him out for the autumn."

McEvoy said Alpine Eagle would need four to six weeks recuperation before being given a slow build-up for his return.

The five-year-old has not won since he took out the 2015 Group Two Autumn Classic in February last year after which he ran a close second to Wandjina in the Australian Guineas.