The takeover had prompted an unusual November 21 filing by Merck KGaA with a New York state court.
In it, Merck KGaA sought to force Facebook to explain how it lost the page, http://www.facebook.com/merck, and the ability to administer it to Merck & Co, a separate company.
Facebook plans to remove the page until both Mercks agree which company may use it.
"The transfer of the vanity URL Facebook.com/Merck from Merck KGaA to Merck & Co was due to an administrative error," Facebook said in a statement, referring to the website address. "We apologize for any inconvenience this may have caused."
Merck & Co spokesman Ronald Rogers said: "We are going to continue to have a Facebook page. It is an active webpage. We are continuing to look into the matter of the vanity URL."
Merck KGaA did not immediately respond to an emailed request for comment after business hours in Germany.
According to court papers, Merck KGaA had contracted with Facebook in March 2010 for exclusive use of the page, but discovered last month that Merck & Co was using it.
Merck KGaA said the loss of the page deprived it of an "important marketing device." Merck & Co was not a defendant.
According to Merck KGaA, the Mercks became separate companies under the Treaty of Versailles. Each retained rights to the Merck trademark in different geographic areas, as part of Germany's reparations following World War I.
The case is Merck KGaA v. Facebook Inc, New York State Supreme Court, New York County, No. 113215/2011.