Manager Terry Collins, reached in Kansas City, said Gee had experienced numbness in his fingers. After extensive testing Monday, Gee was found to have a clot in an artery which doctors at New York's Presbyterian Hospital used a catheter to break up.
Gee, 26, will remain hospitalized to ensure the clot is fully resolved.
Dr. Sharif Ellozy, a vascular expert and associate professor of surgery at The Mount Sinai Hospital who did not examine Gee, offered some insight into the recovery for someone who went through a procedure similar to Gee's.
"You can get up and start moving within a day or so," he told ESPNNewYork.com Tuesday. "As far as him going back to pitching, it depends on what the artery looks like -- if the artery looks normal or if they think there's some abnormality in the artery that caused it. The fact that he's a pitcher and that it was in the arm that he was pitching from, you suspect there may be some injury where it goes between the clavicle and the first rib in that arm. How soon he'll be able to return depends on what they find."
The team announced Gee, who was scheduled to start Friday at Atlanta, will be placed on the disabled list and his return to baseball activity is undetermined.
Gee pitched well in his final start before the All-Star break on Saturday, limiting the Chicago Cubs to one run over eight innings in a 3-1 win. The right-hander is 6-7 with a 4.10 ERA in 17 starts.
Gee has been a mainstay in the rotation for the Mets (46-40), who were a bit of a surprise in the season's first half. They are in third place in the NL East, 4½ games behind the division-leading Washington Nationals.
"I consider him a good friend,'' Mets pitcher R.A. Dickey said from the All-Star Game in Kansas City. "Obviously, what's come out publicly is concerning. It transcends baseball. You want him to be OK because you want him to be OK. Forget what it means to the Mets in this moment.''
"It's very shocking,'' Collins said. "The one thing we said from the beginning is, 'We have to keep our rotation intact.' When we lost [Mike Pelfrey], we were fortunate that we had Chris Young coming. But this is a big piece, because Dillon Gee was pitching good, really good. We've got a big hole to fill right now.''
Collins said veteran Miguel Batista will assume Gee's spot in the rotation for the short term. The Mets will continue to monitor the progress of former first-round pick Matt Harvey, who is 7-4 with a 3.39 ERA in 18 starts at Triple-A Buffalo.
Santana originally was scripted for the second-half opener, but a twisted right ankle scrapped those plans. Gee was due to take Santana's spot Friday before he had the medical emergency arise.