The tribunal stated that the "controversial monies received by the employees were not paid to them as their absolute entitlement".
Rangers had argued that the payments, thought to be close to £49million, had been loans rather than wages and not subject to tax.
No verdict on any sum that the oldco Rangers were liable for was included in the findings, but Sir David Murray's company welcomed the verdict as vindication of their stance.
Oldco Rangers had previously stated they could be liable for up to £75million but the tribunal ruled that Her Majesty's Revenue and Customs assessment should be "reduced substantially" with only some payments subject to tax.
Murray International Holdings, who were majority shareholders of the oldco club until Craig Whyte's takeover in May 2011, declared in a statement: "We are satisfied that the Tax Tribunal has now published its widely awaited decision and note the contents thereof.
"We are pleased with the judgement which leaves minimal tax liability and overwhelmingly supports the views collectively and consistently held by our advisers, legal counsel and MIH itself."