The Financial Times reports armed forces with the Security Service of Ukraine raided the offices in connection with an investigation into allegations Naftogaz had taken illegal transfers of natural gas.
Lawmakers loyal to Prime Minister Yulia Tymoshenko said customs officials were arrested by state security agents, who are allied with President Viktor Yushchenko.
Disputes between Naftogaz and Russian energy monopoly Gazprom over arrears and gas contracts disrupted gas supplies in January. The row left Europe starved for gas as Russia is a major supplier through Ukrainian transit routes.
Tymoshenko said Wednesday that Naftogaz was cleared by customs officials to take ownership of 388.5 billion cubic feet of natural gas at special pricing from Gazprom.
Tymoshenko and Yushchenko are at odds over a variety of issues, and the Financial Times report said the raid may be a manifestation of that standoff.
Naftogaz had warned in February of a renewed gas conflict with Gazprom stemming from a $400 million payment due Sunday. Naftogaz said the crumbling Ukrainian economy and arrears from regional utilities complicated the Sunday deadline.
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