Mr Kenny's special adviser Angela Flanagan signed off on a list of proposed locations that included Swords and Balbriggan – both in Dr Reilly's constituency – in an email written less than two hours before they were due to be announced on July 17.
Newly released records show that the clinics in Dr Reilly's constituency were directly approved by the Taoiseach's office along with the other locations being announced that day.
Former Junior Minister Roisin Shortall – who had responsibility for primary care centres – resigned last year over the decision to locate two of the centres in Dr Reilly's own constituency.
The release of documents showing the involvement of the Taoiseach's top advisers in the primary care clinic saga comes as Dr Reilly has found himself engulfed in fresh accusations that he fast-tracked hospital developments in other ministers' constituencies.
The embattled Dr Reilly was previously accused of "blatant stroke politics" by Ms Shortall when it emerged that Swords and Balbriggan had been added to the list of locations the evening before the announcement of a government stimulus package that included the clinics.
The addition of the two locations occurred amid a flurry of correspondence between the Department of Health and the Department of Public Expenditure and Reform to finalise the locations on the list in the hours leading up to the announcement to be made by the Minister, Brendan Howlin.
The records show that the Taoiseach's office was also sent a list of the proposed clinic locations.
The correspondence also shows that Mr Howlin's department sent a further update to Mr Kenny's advisers on the morning of July 17, stating that Kilkenny was also being added to the list, replacing Castlecomer.
It was at 12.20pm that Mr Kenny's adviser, Ms Flanagan, emailed two of the Taoiseach's other advisers, Andrew McDowell and Paul O'Brien, as well as Mr Howlin's adviser, Ronan O'Brien.
She wrote: "The below list sent regarding primary care centres is perfect and final." The locations for 35 primary care centres were announced by Mr Howlin as part of a government stimulus package later that afternoon at 2pm.
None of the relevant government departments wished to comment.