Anne Frank, a Holocaust victim, gained international fame when her diary was published after her death. Her father, Otto, survived the war and publicized his daughter's diary. He died in 1980.
The Switzerland-based Anne Frank Fonds had lent other documents written by Otto Frank to the Frank Foundation, which is based in Amsterdam, Dutchnews.nl reported.
The Fonds wants the Frank Foundation to return to documents so that it can include them in a new Family Frank Center due to open in Frankfurt in 2016.
But foundation representatives are refusing to hand over the documents and said there is still a legal dispute over who legally owns the papers.
The Fonds went to court in Amsterdam in 2011 in an effort to recover the files, Dutchnews.nl said.
The court ruled that the Fonds must prove it is the legal owner, which it has not yet done.
The two organizations used to work together, Dutchnews.nl said, and were originally planning to house the entire archive together in Amsterdam.
Foundation director Ronald Leopold said he did not know why the Fonds representatives changed their minds.