The move follows Wednesday's raid of the head office of Naftogaz by the SBU security service, overseen by Ukrainian President Viktor Yushchenko.
Security service officers were reportedly demanding the original copies of the company's January gas deal with Russia's Gazprom, following accusations that Naftogaz had illegally diverted large volumes of gas bought from Russia.
Ukrainian Prime Minister Yulia Tymoshenko, who oversees Naftogaz, fiercely criticized the raid, saying it was aimed at disrupting payments and causing panic.
Valery Khoroshevskiy, deputy head of the SBU, dismissed on Thursday reports that the raid was aimed at protecting the interests of Swiss gas intermediary RosUkrEnergo.
The SBU had accused Naftogaz of diverting 6.3 billion cubic meters of natural gas and tried to find proofs during the search.
Russia and Ukraine earlier decided to improve the transparency of bilateral gas trade by cutting out trading intermediaries.
