BANGKOK (Reuters) - Ousted Thai prime minister Yingluck Shinawatra can appeal a 35 billion baht ($1 billion) fine imposed on her in connection with a rice-subsidy scheme, the junta chief said on Tuesday in his first public comment since the government ordered the fine.

Critics say the scheme, which paid farmers above-market rates for their rice, hemorrhaged billions of dollars.

Yingluck, whose government was ousted in a May 2014 military coup, was charged with criminal negligence over the rice scheme, a flagship policy of her administration, and is now fighting the charges in court.

She told reporters on Friday that she had received a notice ordering her to pay the $1 billion fine.

Prime Minister Prayuth Chan-ocha, who is also head of the junta, said that Yingluck can appeal the order and denied that the military government was singling her out.

"If there is anything to clarify, then do that in court," Prayuth told reporters. "Don't do it through the media," he said, referring to comments given by Yingluck to reporters about the fine.

"I'm only responsible for bringing it into the justice system. I'm not one to say it is right or wrong, though there was a lot of damage caused," Prayuth said.

Yingluck has repeatedly denied negligence and vowed last week to use "every channel available" to fight the fine.

She has 45 days to appeal the order.

The rice scheme was a populist policy engineered by Yingluck's brother, former prime minister Thaksin Shinawatra, who was toppled in a 2006 coup and is living abroad to avoid a two-year prison sentence handed down in 2008 for graft in a land purchase case.

Supporters of Yingluck and Thaksin say the case against Yingluck is part of a military plan to wipe out the influence of the Shinawatra family.

The Shinawatras have dominated Thai politics for more than 15 years and still command loyalty in the largely agrarian north and northeast of the country.

(Reporting by Aukkarapon Niyomyat; Writing by Patpicha Tanakasempipat; Editing by Amy Sawitta Lefevre and Nick Macfie)