Gee was taken to the hospital in New York after experiencing numbness in his fingers and was scheduled to undergo several tests including an angiogram and MRI on Monday when the clot was discovered.
Gee, 26, is 6-7 with a 4.10 ERA this season and 21-15 in his career. He was scheduled to pitch in one of the opening games this weekend in Atlanta.
The best-case scenario for the Mets would be Gee missing only one start. Because he pitched July 7, the move made retroactively makes him eligible to return July 23.
Tentatively, veteran right-hander Chris Young is scheduled to start for the Mets in Friday's series opener at Atlanta.
Left-hander Johan Santana (ankle) was sore after his last start but the pitcher and the Mets both said he wouldn't miss a turn in the rotation. He's the probable starter for Friday's series opener at Turner Field provided a long-toss session Tuesday or Wednesday goes well. If the Mets exercise extra caution despite Santana's poor history coming off extended rest, Young will start.
Santana left his last outing before the All-Star break on Friday in the fifth inning with a slight ankle sprain.