The investigation by the Strasbourg-based official related to a complaint made by Testbiotech, a German Institute for the Independent Impact Assessment of Biotechnology, against the Commission and its management of publicly funded risk research projects.
The EU watchdog decided that there was "no clear evidence" for maladministration by the Commission.
However, O'Reilly, who investigates alleged maladministration by EU institutions, supports Testbiotech's argument that the Commission should "consider a fuller and more thorough" explanation of why it believes that links between industry and scientists do not create conflicts of interest.
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The Irish-born official said that, in future, the names of experts involved in the evaluation of specific research topics should be published along with their declarations of interests.
The complaint, first made in March last year, was triggered by a publicly funded research project called GRACE which aimed to investigate the risks of genetically engineered plants.
Testbiotech claimed in several reports that "industrial nepotism appeared to be prevalent within this project."
In November 2015, Testbiotech said it had evidence of similar problems with other EU projects in the same area.
Nevertheless, the Commission rejected the Testbiotech findings without giving any detailed reasons.
However, Christoph Then, of Testbiotech, said, "The decision made by the Ombudsman implies that substantial changes are necessary for the future."
He added, "There is a general problem with a strong bias in the risk research and risk assessment of genetically engineered organisms that favours industry. There are multi-layered links to the biotech industry.
"And the problem cannot be reduced to payments for specific experts. For example, intellectual bias is significant in the activities of organisations that have a strong affiliation to industry."
"Similarly, the struggle to find funding is of major relevance", said Then.
"In reality, health and the environment are not given much priority.
"The problem with bias in risk assessment not only concerns specific research projects, but also research institutions and the relevant EU authorities," he said.
"For example, the European Food Safety Authority (EFSA) has been repeatedly confronted with issues relating to conflicts of interest within its expert panels. And up to now, EFSA could not find a convincing solution.
"Just recently, the executive director of EFSA, Bernhard Url, suggested that while payments from industry to EFSA experts should be regarded as a conflict of interest, their 'intellectual bias' should simply be ignored in future."
He continued, "Looking away or intentional ignorance means that these problems simply get bigger and bigger.
"It is time for a change."
He said that implementing the decision of the Ombudsman could be "an important first step."
"We have to take measures to prevent science from becoming abused by industry. What we need in addition to transparency are strict and clear rules to avoid conflicts of interest."