Valentin Mondriyevskiy said Ivchenko had filed to leave his post after winning a seat the Supreme Rada, Ukraine's parliament, in March.
Ivchenko, also head of the Congress of Ukrainian Nationalists, ran for parliament in the March 26 elections within pro-presidential bloc Our Ukraine, which won 81 seats.
Naftogaz press secretary Eduard Zanyuk confirmed the resignation Thursday, saying Ivchenko had chosen to focus on his parliamentary duties.
"Oleksiy Ivchenko made a voluntary decision to leave the post of board chairman in the company and filed an application. This was his decision," the company said.
Earlier on Thursday, Ukrnaft shareholders made a decision to relieve Ivchenko as chairman of the oil company's supervisory board.
Ivchenko was appointed board chairman of Naftogaz in March 2005.
Naftogaz, which accounts for 10% of the state budget's revenues, is facing serious financial problems. Ivchenko said in late April the company's losses in 1Q06 had hit $500 million.
He clashed with the Finance Ministry, which rejected Naftogaz's proposal to raise gas prices for households by 60% starting from July, and said the company's tax arrears stood at $118 million.
The Finance Ministry demanded instead that Naftogaz scale back spending on a number of foreign projects and cut investment in production in Ukraine.
Ivchenko accused the government of reluctance to address problems facing the company, saying such an approach was "tantamount to a crime."
