CAIRO, Oct 28 (Reuters) - A comedian who outraged Egypt's now deposed Islamist rulers with his satirical TV show is to be investigated by the current army-backed government, a state-run newspaper reported on Monday.

Bassem Youssef, often called Egypt's answer to U.S. satirist Jon Stewart, returned to the airwaves on Friday for the first time since the army ousted Mohamed Mursi, the Islamist president he used to lampoon in jokes and song-and-dance routines.

Youssef turned his comic jibes on the new government, joking about the popularity of army chief General Abdel Fattah al-Sisi and implying that no one had heard of interim President Adly Mansour.

The programme was enough for public prosecutor Hisham Barakat to launch an investigation, after a viewer complained that it had harmed the public interest and risked creating chaos in the country, Al-Ahram newspaper reported.

Youssef, who was arrested under Mursi's government and appeared in court on charges - later dropped - of insulting the president and Islam, carefully poked fun at various political camps in Friday's broadcast, but stopped short of an outright assault on Sisi, whose image adorns posters across Cairo.

His arrest under Mursi was criticised by liberals who said the 2011 uprising that toppled Hosni Mubarak was going back toward autocratic rule.

With a new military-backed government in place, activists say similar assaults on press freedom and on other civil liberties like the right to protest, seem all too likely.

"I am not with the (Islamists), who attacked us and called us heretics ... and publicly called for our imprisonment," Youssef said on his Friday show.

"At the same time, I am not with hypocrisy, deification of individuals and creation of pharaohs," Youssef said. "We are afraid that fascism in the name of religion gets replaced with fascism in the name of nationalism."

Mursi's ouster on July 3 was followed by the worst violence in Egypt's modern history, including the violent clearing of Muslim Brotherhood protest camps in which hundreds of the group's supporters were killed.

Thousands more, including the movement's leadership, have been arrested.

(Reporting By Maggie Fick; Editing by Robin Pomeroy)