The 26-year-old has lost a third of his body weight since being imprisoned, his doctor says that his organs are at risk of failure and he could "die within a few days.".
"He has started to have impaired liver and kidney function," said Doctor Mohamed Osama el-Homsi. "It means that his organs are in danger."
El-Homsi said el-Shamy's hunger strike has surpassed all records and he is encouraging him to abandon the fast.
In a letter from prison two weeks ago, the journalist said he had been questioned for two consecutive days by guards trying to get him to give up the strike.
El-Shamy was moved from his cell in Tora prison to an undisclosed location, after his lawyer requested he be transferred to a hospital.
He has been in prison since August 14, after he was arrested for covering a violent police raid at a mosque in Cairo where supporters of deposed President Mohammed Morsi were holding a sit-in.