The son of Nathaniel was the runner-up in the Queen's Vase at Royal Ascot and showed improved form when landing the Group Three Geoffrey Freer at Newbury last month.
However, the colt has suffered a setback which will see him miss the Doncaster Classic.
Meade said: "It is just unfortunate. Yesterday he sustained a soft tissue injury which is going to rule him out for the rest of the season, I'm afraid.
"It was right at the 11th hour, which is so sad for everybody.
"He won the Geoffrey Freer convincingly and he looked to have every chance of running a big race at Doncaster.
"It looked a good opportunity, but he just had a little niggle that we investigated and unfortunately, with the timing of it, he is going to be off for the rest of the year."
Owned by Aquis Farm and Manton Park, Zechariah's future may be in the southern hemisphere.
Meade added: "There is every chance he will go to Australia. We see him as a Cup horse, so those sort of targets must come into consideration.
"It is early days and we will see how his rehabilitation goes, and then make a plan through the winter.
"It is galling for the whole team. We have a small team and to have those high-profile runners is so important. It is upsetting for us and when you are with these horses every day and something goes wrong, it is very upsetting.
"Any chance of having a runner in a Classic is always hard to come by."
Meade also had news of Lone Eagle, who has been on the comeback trail this season after suffering a serious leg injury in the King George VI And Queen Elizabeth Stakes at Ascot last year.
The son of Galileo, who finished a neck second to Hurricane Lane in last season's Irish Derby, has recovered well from a cracked fetlock and after making a return at Goodwood in May, was fifth to Alpinista in the Grand Prix de Saint-Cloud in early July.
Lone Eagle holds entries in both the Long Distance Cup and the Champion Stakes at Ascot next month.
Meade said: "I think Champions Day is the target and we seem to be having a bit of rain now, and that seems to be the plan with him."