After leaving politics, O'Mahony became a public affairs consultant in 1989. He is also an Associate Lecturer in European Studies at the Institute of Public Administration in Dublin.
O'Mahony, later became known as the "public face" of the Irish Tobacco Manufacturers Advisory Committee (ITMAC), of which he was director and which shared an office in Dublin with O'Mahony's company CIPA, and in 1992 O'Mahony's name was recorded as the donor of IR£3,000 donated to the Progressive Democrats on behalf of ITMAC. As a lobbyist against plans for legislation to protect workers against passive smoking, O'Mahony was named in 1999 as having been involved in lobbying by ITMAC which Dr Fenton Howell, vice-president of the Irish Medical Organisation, claimed "secretly manipulated and misled a group advising the minister for health on new smoking regulations". O'Mahony subsequently told the Joint Oireachtas Committee on Health and Children that he could not remember who gave him information about a meeting of a Department of Health working group which had allowed him to circulate a report of the meeting to tobacco companies within 24 hours of the meeting. After hearing O'Mahony's evidence, the chairman Batt O'Keeffe, told Mahony that some of the points made about his conduct were "well-founded", and recommended that "in future deliberations he would be conscious of the public interest and people's health". In 2001, Howell told a sub-committee that O'Mahony had been "less than candid in his replies" to the committee.
O'Mahony was one of three former senior officials of the Irish Labour Party reported to have had ties with the tobacco industry.
^"15 years of crisis, achievement and controversy take their toll". The Irish Times. 6 November 1997. Retrieved 11 February 2008. "Internally he [Spring] lost a battle over the procedure to be used in selecting two replacement Dublin MEPs. Two anti-coalitionists, Brendan Halligan and Flor O'Mahony, won the contest. … The party was hammered in the Dublin Central by-election of 1983. In 1984 it lost all four European Parliament seats it had won in 1979"