Speaking to Reuters, Olga Beloblovskaya said she had no more more details about the investigation, but said Dragon Capital had always operated within the limits of the law.
"They have a court order to remove computer equipment. They say it's about the illegal use of software. But the firm bought this programme legally and officially. They want to take all the computers and paralyse our work," she said in a Facebook post.
The SBU did not immediately respond to requests for comment.
Ukraine has struggled to shake off a reputation for endemic corruption and businesses often complain of harassment from law enforcement bodies and the tax revenue service.
Read alsoGroysman informed about searches in Dragon CapitalPrime Minister Volodymyr Groysman interrupted a televised cabinet meeting to express his surprise at the news of the raid, which he warned could affect investor sentiment.
"I don't have the right to meddle in the work of the SBU, but I think that everything should be done properly, without paralysing (Dragon Capital's) work," he told ministers.
"This doesn't help to build the investment climate," he said.