"In light of the difficult financial situation the club has voluntarily decided to play (in Russia's second division)," Amkar said on their website.
"As of today, the club has accumulated debt of 167 million roubles ($5.43 million) and negotiations with potential sponsors have not materialised."
Amkar, whose president Valery Chuprakov resigned on Tuesday, said they had sent an official letter to the RFPL, informing the league of the decision to pull out.
Amkar, who just avoided relegation this year after finishing in 14th place, become the second club to pull out of the Russian top flight in less than a year.
Fellow stragglers FK Moscow were disbanded in February after their main sponsor Norilsk Nickel withdrew its financing.
Norilsk, the world's biggest nickel and palladium producer, said at the time it would no longer finance the team because it was too far from the company's base in the Siberian city of Norilsk, 3,000 kms northeast of Moscow.
Amkar's financial problems are a big blow to Russia's soccer image after the world's largest country was awarded the right to stage the 2018 World Cup earlier this month.
Several other Premier League clubs have also struggled to maintain their position in the top flight.
Last year, Siberian club Tom Tomsk were saved from going out of business because of mounting debt following the intervention of Prime Minister Vladimir Putin, who ordered seven of Russia's largest oil and energy companies to rescue them.
