The Swiss firm was seeking European marketing approval for Alpheon, a "biosimilar" version of Roche's Roferon-A, an injectable interferon used to treat hepatitis C.
However, the approval process for copycat biologics is complicated because of the challenges posed by the sophisticated manufacturing processes of biologic drugs.
Biogeneric active pharmaceutical ingredients (APIs) have to be re-developed using living cells, and so the right cell lines have to be found to produce an API that is as much as possible identical to the original supplier' s API, without infringing only one of the many application patents.
The EMEA's Committee for Medicinal Products for Human Use (CHMP) finally rejected Alpheon as being adequately biosimilar after a 204 day review.
"There were major concerns regarding the comparability of Alpheon and Roferon-A, due to differences, such as impurities, identified between the two drugs," wrote the agency in a statement.
"There were also concerns that BioPartners did not have enough data on the stability of the API and of the final drug product. In addition, the process used for making the drug had not been adequately validated."
In the data presented by BioPartners, the number of patients with hepatitis C responding to treatment with Alpheon and Roferon-A was similar in the clinical study.
"However, some differences were seen between the two drugs: more patients experienced a return of the disease after treatment with Alpheon was stopped than with Roferon-A and there were more side effects with Alpheon," said the CHMP statement.
In addition, CHMP said the test used in the study to investigate the potential for the medicine to trigger an immunological response had not been sufficiently validated.
"At this point in time, the CHMP was of the opinion that Alpheon could not be considered as a biosimilar medicine of Roferon-A, and hence recommended that Alpheon be refused marketing authorisation."
Some of the biggest-selling biological drugs developed during the first phase of the biotechnology revolution in the 1980s have already lost or will lose patent protection in the next few years.
Products such as insulin, human growth factor, epoetin, colony stimulating factors, interferon alpha and interferon beta are now particularly exposed and with a combined value of $20.2bn (€16bn) in global sales, these drugs are becoming fair game for a growing number of biogenerics companies such as BioPartners.
Only last month BioPartners was successful in gaining approval for its biosimilar growth hormone drug Valtropin, making it only the second biogeneric drug to have been approved in Europe and the company has released a statement expressing its "disappointment" over the latest rejection.
"We are looking forward to evaluating the EMEA report and with the issues clarified, anticipate being in an even better position for resubmission," said the statement.
The firm now has 15 days in which to ask for a re-examination of the opinion.