The trust, in Staffordshire, has been in administration for seven months after the transfer of a £134m pension debt from the collapse of the pottery firm.
It was placed into administration in April this year by the Pension Protection Fund, the body established to protect pension payments to members of defined-benefit pension funds. The fund wants to sell the museum’s assets to reduce the pension fund debts.
The trust, which had five employees enrolled in the company’s 7,000-member scheme, was the only body contributing to the scheme that was not in administration, and therefore became liable for the entire debt.
The museum’s share of the shortfall, based only on its own employees, would have been about £60,000.
It asked the Charity Commission whether the collection was a permanent endowment, which might have meant it could not be sold to pay off the Wedgwood Group Pension Plan deficit.
A commission spokeswoman said: "The Charity Commission is aware that the Wedgwood Museum Trust has been placed into administration and we have a great deal of sympathy for the position in which the trustees of the charity find themselves.
"The commission was asked to provide advice on whether the Wedgwood Collection is held as permanent endowment and might therefore be protected, or whether it is part of the charitable company’s corporate property that is available to creditors.
"Unfortunately it is our considered view that the museum’s collection is not protected."
The status and value of the collection are expected be decided in a court case, which the administrators say is likely to take place next January.