Bayliss says players are at risk of a "blow out" due to the amount of games they are playing across all three formats.
The Yorkshire seamer suffered a recurrence of a hamstring strain during the Twenty20 defeat against New Zealand in Wellington.
Stokes, 26, was withdrawn from England duty in September 2017 after he was arrested on suspicion of causing actual bodily harm.
Buttler said the shortest format is "going from strength to strength" and warned that it could eventually establish a "monopoly" over the sport.
Morgan, 31, missed England's defeat against Australia in Melbourne due to a groin injury picked up in training.
Morgan sat out England's Twenty20 defeat against Australia in Melbourne, with James Vince taking his place.
Morgan said his batsmen had the right idea in taking the attack to Australia's bowlers but added that the execution was wide of the mark.
White-ball specialist Glenn Maxwell scores an unbeaten 103* to add to his bowling figures of 3-10 as England succumb to a five-wicket loss to Australia in their tri-series opener.
Eoin Morgan's side face Australia in their opening match of the Twenty20 tournament in Hobart on 7 February.
Roy missed the warm-up game against the Prime Minister's XI last week with a back spasm, while Plunkett has been out of action with a hamstring problem.
Seamers Liam Plunkett and Chris Jordan are nursing hamstring injuries and are doubtful to play in the warm-up game against the Prime Minister's XI.
Chennai Super Kings and Rajasthan Royals will return to the upcoming season of the domestic T20 league that will take place in India after completing their two-year suspension.
Jos Buttler and Chris Woakes produce a superb seventh-wicket stand of 113 runs as England take an unassailable 3-0 lead in their five-match ODI series against Australia.
Test captain Joe Root scores 46 not out and takes two wickets for 31 runs as England secure a comfortable four-wicket ODI victory over Australia at The Gabba in Brisbane.
Ben Stokes will be considered for England selection is expected to join the squad for the T20 matches against New Zealand in February.
Ben Stokes has been charged with affray relating to an incident that took place outside a Bristol night club in September 2016.
The Surrey batsman hits a brilliant 180 as England claim seven-wicket win in first ODI in Melbourne.
India's captain was dismissed for just five runs in the first innings of the Test against South Africa on Friday.
Bayliss, who took over as England coach in 2015, faced questions over his future after the Three Lions surrendered the Ashes urn to Australia.
England's second innings ended at 180-9, with captain Joe Root retiring hurt on 58 due to a stomach bug, as the tourists lost by an innings and 123 runs.