A total of 391 lawmakers in the 450-seat Supreme Rada voted in favor.
The SBU security service, overseen by President Viktor Yushchenko, raided the company as it was due to make a payment for Russian natural gas. The service has accused Naftogaz of illegally diverting 6.3 billion cubic meters of gas bought from Russia.
Prime Minister Yulia Tymoshenko, who oversees Naftogaz, fiercely criticized the raid, saying it was aimed at disrupting payments and causing panic.
The agents searched for the original copies of January's gas deal with Russia, but Naftogaz later said they had left without the documents.
On Thursday, the Security Service searched the main office of Ukrtransgaz, Naftogaz's affiliate that runs the country's pipelines, despite a court ruling that had barred any investigation.