"The commission qualifies the incident as deliberates action of unidentified persons," the source said.
The source explained to Sputnik that Soyuz had one-off production, the spacecraft was assembled manually, and therefore some details were adjusted to each other during the assembly, for example, with a file, but a drill was never used as all holes were made with press molds.
Earlier in the day, a source told Sputnik that the commission had to determine the cause of the incident within two days and prepare a report for Roscosmos head Dmitry Rogozin.
However, the source was certain that the work could not be finished by Friday, and the experts would have to continue into the weekend.
According to Roscosmos, the results of the investigation will be made public by mid-September.
The internal commission mainly includes representatives of the factory within Energia, which is responsible for the production of spacecraft, the source said. The panel began its work on Monday and has been holding daily meetings in Energia in the mornings, while the experts have been working in production facilities in the afternoons.
"The factory has practically stopped operating. All production facilities are being checked, managers are constantly at the meetings," the source said.
According to another source, the hole had to have been made at the final stages of production, at the very least after the ship was painted.
The source said that the two main scenarios were being considered by the commission: a specialist wanted to do something that was not in the plan and secured an agreement with the foreman to do the adjustments off-the-books, or some loner may have entered the facilities.
"The latter scenario raises a lot of questions about the quality of work done by the facilities' security team," the source told Sputnik.
Last week, Rogozin said an air leak and subsequent drop in pressure occurred at the Soyuz spacecraft. The ISS crew were able to fix the problem.
A source told Sputnik on Tuesday that Energia would check all the Soyuz and Progress spacecraft that were prepared for launch.