BANGKOK, June 12 (Reuters) - Thailand's prime ministerial frontrunner Pita Limjareonrat will be investigated over whether he was qualified to run in last month's election, a top official said on Monday, in another setback as he battles to win backing for his premiership.

Pita, the 42-year-old leader of the progressive Move Forward party whose election victory stunned Thailand's military-backed establishment, has faced multiple complaints from rivals, three of which the poll body has dismissed for late submission, while four others against the party have been thrown out.

But Pita is by no means in the clear, with the commission looking into whether he was knowingly unfit to register as a parliamentary candidate because of his ownership of shares in a media firm, which is prohibited under election rules.

Pita has downplayed the issue, arguing the shares in the firm, ITV, have since been transferred and the company was not an active media organisation. He faces disqualification, up to 10 years in jail and 20 years banned from politics if found in violation.

"There is sufficient information to suspect that the candidate is unfit or prohibited from seeking public office, according to electoral regulations, to further investigate Pita," election commission chairman Ittiporn Boonprakong told Reuters in a text message.

The opposition Move Forward and Pheu Thai parties thumped conservative opponents allied with the military in a resounding rejection of nearly nine years of government led or backed by the army after its 2014 coup.

They have formed an alliance with six smaller parties, but Pita's bid to be premier and form the government is expected to face resistance in a conservative-leaning Senate that was appointed under the military. A bicameral vote on a prime minister is expected by August, with weeks of uncertainty ahead.

Move Forward's anti-establishment agenda clashes with the interests of a royalist military and old-money business elite that has influenced politics for decades in Southeast Asia's second biggest economy.

The party won huge support among the youth and the capital Bangkok with a platform of institutional change, including reducing the army's political role, undoing monopolies and reviewing a controversial law against insulting the monarchy.

Asked about challenges against Move Forward, its secretary-general Chaitawat Tulathon on Monday said the voice of the people will be protected.

"The election commission may take action against Pita in the future," he told a press conference.

"The party is confident that the allegations do not have sufficient evidence."