Speaking in Brussels on Wednesday, the Irish official said the executive had "failed to make a convincing case" for refusing to crack down on the industry's influence on EU decision making.
The Strasbourg-based watchdog also castigated the tobacco sector, saying its products contributed to the deaths of some 700,000 Europeans every year.
She said, "The biggest number of complaints I receive are about who has what influence on decision making at EU level. It is all about transparency."
O'Reilly, who was addressing a conference she organised on 'improving transparency in tobacco lobbying', said the Commission's refusal to take specific measures to tackle tobacco industry lobbying influence reflects a worrying complacency and lack of vigilance regarding the large-scale lobbying efforts of this sector.
Last October, the official upheld a complaint by the Brussels-based Corporate Europe Observatory (CEO) against the Commission over its failure to implement UN tobacco lobby rules.
An investigation by the official involved an inspection of official files and staff agendas at the Commission's HQ, the Berlaymont, to identify possible meetings with tobacco lobbyists.
The Ombudsman's investigation found that a top official from the Commission's legal service had declared no meetings with tobacco industry representatives despite having meetings with a lawyer working for tobacco giant Philip Morris.
The Commission's contacts with the tobacco industry attracted major controversy following revelations of heavy lobbying pressure during the 2012-2014 revision of the EU's tobacco products directive, including the 'Dalligate' scandal, which involved the forced resignation of then EU health commissioner John Dalli in October 2013.
Deeming the Commission's failure to comply with the World Health Organisation's (WHO) Framework Convention on Tobacco Control as 'maladministration', O'Reilly at the time urged the Commission to publish details of all meetings with tobacco lobbyists online and asked the Commission for an update on its promise to introduce a mandatory transparency register for lobbyists.
However, she told the conference that only one Commission directorate, DG health, had so far complied with her request.
"The Commission rejected my recommendations. It has failed to make a convincing case for refusing to do so, something I find puzzling. That is why, today, I am calling on all other Commission DGs to follow the example set by DG Sanco and divulge details of all meetings between Commission staff and representatives of the tobacco industry."
The Commission argues that additional transparency measures are not needed because meetings between top officials and tobacco lobbyists have been scaled back since the legislative process around the tobacco products directive came to an end.
The Ombudsman also defended her decision not to invite anyone from the tobacco industry to speak at the conference, saying, I know the industry is unhappy with this and has said that it feels discriminated against but it is my decision."
Reacting to her comments, European health Commissioner Vytenis Andriukaitis sought to defend the college's role but agreed that he would also like to see other DGs publicise details of contacts with the tobacco sector.
The Lithuanian admitted that the aims of the EU - to reduce tobacco consumption - and those of the industry were "quite incompatible" and that the commission continues to come under "heavy lobbying pressure "from the industry to influence ongoing legislation.
He said, "As a medical doctor I know all too well the perils of tobacco and the harm it causes. Tobacco kills one in four Europeans every year.
"But I stress that, in my DG, every effort is made to ensure that decisions are not subject to undue influence from the industry. Staff must behave with the utmost integrity, there are strict rules on access to documents and all meeting with industry representatives are published online."
Denying that his department had received many approaches from tobacco lobbyists, he added, "Yes, I would like the rest of the Commission to follow the example set by my DG and keep all contact with the industry to a minimum.
"I want to stress that I believe the industry products that are absolutely against public health."
Further comment came from Roberto Bertollini, chief scientist at WHO representative to the EU, who told the packed debate that despite the adoption of the EU's tobacco products directive, the industry still sought to exert "pressure and influence" on decision making.
He said, "Such attempts to push their products and exert influence in certain areas, such as employment, are still being made by the industry.
"The Commission has a leadership role to play here but, clearly, the efforts made by certain DGs are not shared by other ones."
Speaking separately, Olivier Hoedeman, research and campaigns coordinator, Corporate Europe Observatory, said, "The Commission's stubborn rejection of the Ombudsman´s recommendation to secure tobacco lobbying transparency in line with UN guidelines is a major missed opportunity. If the
Commission does not even take the risks of undue lobbying influence seriously for this most controversial sector, then how can the public have any trust in its overall ability to protect the public interest against regulatory capture and undue influence?”
"All of this does not bode well for transparency and accountability, which Commission President Jean-Claude Juncker announced as a priority for his Commission upon taking office. Since then we've seen these issues constantly put on the back burner."