The move follows allegations by a lobby group opposed to all animal testing claiming that a Commission task force on non-primate research lacked relevant expertise.
The European Coalition to End Animal Experiments (ECEAE) says the EU executive failed to take some evidence into account, prompting the Ombudsman to examine whether the Commission is guilty of "maladministration". The Commission must give its side of the story by 30 April.
Diamandouros said the issue is of great interest to the general public and noted that the Lisbon Treaty commits the EU institutions to maintaining open and regular dialogue with civil society groups.
The complaint stems from a report by the Scientific Committee on Health and Environmental Risks (SCHER) which the Commission asked to consider the merits of alternatives to non-human primate research.
In October 2008, the Commission organised a public hearing on the issue but a number of animal protection, medical and patient safety organisations complained that the process had been unfair.
The ECEAE subsequently lodged a formal complaint with the Ombudsman's office in May 2009, charging that the SCHER group did not have sufficient expertise in non-primate experimentation and that the Commission had ignored much of the evidence supplied by animal rights advocates.
The Ombudsman has asked the Commission to detail how the experts of the working group were selected. He also wants to know the basis on which the Commission concluded that SCHER had considered all relevant contributions from third parties.
Michelle Thew, chief executive of the ECEAE, welcomed the inquiry but said she was disappointed the Ombudsman had taken so long to act.
In a statement she said that even if the complaint is upheld it may be too late to have any impact on animal testing legislation, which is currently under review.
"It is truly unforgivable that the European Commission should come up with such a one-sided and unscientific report, from a working group packed with inexpert animal researchers," Thew said.