Doctors operated to alleviate a blockage in Pataki's digestive system, said his spokesman, David Catalfamo.
Afterward, the governor was "awake, alert and resting comfortably," Catalfamo said in a statement.
Pataki, 60, checked himself into Hudson Valley Medical Center last Thursday complaining of severe abdominal pain. His appendix, which had begun to rupture, was removed during emergency surgery.
The governor was expected to be released Saturday, but his condition did not improve, so he was transferred to New York Presbyterian Hospital in Manhattan where doctors have access to more resources, Catalfamo said.
A blockage following abdominal surgery is relatively rare, said Daniel Herron, an assistant professor of surgery at Mount Sinai Medical Center in Manhattan.
Pataki, a three-term Republican, is considering a run for president in 2008.
Fellow GOP Gov. Ernie Fletcher of Kentucky also remained hospitalized Tuesday after contracting a blood infection while recovering from gallbladder surgery last week. The bacteria in Fletcher's blood were moderately resistant to antibiotics, but treatment seems to be working, doctors said.
In Connecticut, another Republican governor, M. Jodi Rell, was involved in a car accident Tuesday morning but escaped injury. The governor's driver and the teenager whose vehicle hit the car's driver's side were also uninjured, authorities said.