On March 4, masked security agents raided the headquarters of Naftogaz, sparking criticism from the prime minister.
The SBU, which is overseen by President Viktor Yushchenko, has accused Naftogaz of illegally diverting 6.3 billion cubic meters of natural gas bought from Russia.
Following news of the raid, Prime Minister Yulia Tymoshenko said the sole aim of the operation was to "paralyze Naftogaz's activities and destroy the gas distribution system in Ukraine and the system of payments. They wanted to frighten people."
Naftogaz spokesman Valentyn Zemlyanskiy said earlier that during the raid security service agents demanded to be shown all the original documentation relating to the January 19 gas deal between Naftogaz and Russian gas giant Gazprom. However, he said no documents had been confiscated.
Zemlyanskiy said on March 4 that the company accountant had been questioned for five hours by members of the security service, resulting in her being hospitalized with high blood pressure and despite being in hospital she was still being put under pressure by security officers.
The Ukrainian security service said on Thursday it had stopped its investigation into Naftogaz's gas operations after a court ruled the probe was illegal.