While Kings XI Punjab fast bowler Harris has been laid low by a left Achilles tendon injury, Pune Warriors India's Samuels is suffering from a groin injury.
Harris' injury will rule him out of competitive cricket for around two months.
"Cricket Australia today advises that Ryan Harris has an Achilles injury which has meant his return from the Indian Premier League," CA said in a statement.
Harris, however, is expected to be fit for the Ashes series against England scheduled for June-July. "Ryan Harris has returned from IPL duties with Kings XI Punjab with a left Achilles tendon injury," said CA's Chief Medical Officer Justin Paoloni.
"Scans showed the injury was not serious and he will undergo intensive rehabilitation with the aim of him being available to take part in the Australia A Series and we expect he will be fit to play in the Ashes."
Paoloni also gave an update on the injury of pacer Mitchell Starc, who had bone spurs removed from his ankle. "Mitchell Starc is recovering as expected from arthroscopic ankle surgery. Currently he is meeting all clinical timeframes and with this progress the target is to play ICC Champions Trophy and then the Ashes," he said.
Samuels also returned home to Jamaica owing to a groin injury and to be by the side of his mother, who has sustained a knee fracture.
The man of the match of the ICC World T20 final played only two games for Pune this season scoring only eight runs and taking a single wicket.
According to a team sources, since the injury was taking time to heal, Samuels headed back home to be by the side of his ailing mother. However, a possibility remains that the Jamaican might come back to India if Warriors somehow manage to make it to the knock-out rounds.