Clarkson was admitted to hospital on Monday night after experiencing back pain over the past couple of weeks.
After a series of tests, he was diagnosed with GBS, which is an inflammation of the nerves from the spinal cord.
Clarkson began treatment last night and doctors are confident he will make a full recovery.
He will remain in hospital for the next week with a timeline of his recovery yet to be determined.
Assistant coach Brendon Bolton will take the reins in his absence.
"We're fortunate that Alastair's condition has been detected early, and we're confident he is in the best possible hands under the care of very experienced specialists," CEO Stuart Fox said.
"Our primary concern is for Alastair's health and a timeline for his return to coaching is not a consideration at this stage.
"The club will provide support for Alastair and his family for as long as it takes him to recover."
Bolton's appointment as interim coach was decided unanimously by the Hawthorn Board, Fox, Chris Fagan, Alastair Clarkson and Captain Luke Hodge.
"Having worked together for six years, Alastair and Brendon share very similar coaching, teaching and management philosophies," Fox said.
"The club has complete confidence that Brendon can step in temporarily for Alastair for as long as may be required.
"With the support of the other assistant coaches, development coaches, leadership group and players, we are confident Brendon’s transition as temporary senior coach will be seamless."