McCain, a Republican, has been an outspoken advocate for US military aid to the terrorists fighting the government of President Bashar al-Assad and made a short, highly publicized trip to meet militant commanders in Syria three days ago.
McCain may have crossed paths with men linked to a group notorious in the region for kidnapping the pilgrims, the Daily Star said.
The paper said that as well as McCain's photographs with rebel commanders, one image showed the face of Mohammad Nour - identified by two freed hostages as the chief spokesman and photographer for the Northern Storm brigade that kidnapped them.
The image demonstrates the difficulty of identifying who the West might want to deal with and could possibly further inflame the delicate sectarian balance in a conflict that is spilling over Lebanon's borders.
A spokesman for McCain claimed none of the people he met identified themselves as Nour and it had not been his intention to meet anyone of that name.
"If the individual photographed with Senator McCain is in fact Mohammad Nour, that is regrettable," spokesman Brian Rogers said.
"But it would be ludicrous to suggest that the senator in any way condones the kidnapping of Lebanese Shia pilgrims or has any communication with those responsible. Senator McCain condemns such heinous actions in the strongest possible terms."
The hostages were seized in northern Syria as they returned from a pilgrimage in Iran. Lebanese officials flew to Turkey on Thursday in the latest effort to secure the release of the remaining nine hostages.