During this week's minicamp, the Giants announced the hiring of Pat Ruel to help coach the line while Flaherty continues treatment.
"I will continue to coach the Giants' offensive line as long as my treatment makes that possible," said Flaherty in a statement released by the Giants. "I feel good and I look forward to coaching this season as I do every season."
Coughlin said Flaherty's illness was discovered as a result of yearly physicals provided by the Giants for coaches. His treatment will include surgery.
"Because of the nature of the treatment, Pat is going to have a certain amount of down time, and we were fortunate that Pat Ruel was available to help in those situations," Coughlin said.
Flaherty is 48. He had coached in 2000 for Washington, where he helped Stephen Alexander win a Pro Bowl berth. He coached college football from 1980-1999, including a stint in 1982 at Penn State with a national championship team.
Flaherty has a wife, Lynne, and two children: Shawn and Colleen.