"We strongly distance ourselves from the vandalism and would like to apologise to FCI Levadia Tallinn," the club writes on its website.
Pictures posted by the Estonian Football Association show vandalism of, among other things, toilets.
IFK Gothenburg writes that if the club receives fines or other costs, "the association will file a claim for damages against the people who caused them."
It is also written that the incident could affect the team's supporters in upcoming European matches.
IFK Göteborg won the two-legged tie in the Conference League 4-3 and is through to the third qualifying round, where it will face Gent.
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