Lions centre Shanklin has been ruled out for three months and will miss the entire Championship, which kicks-off against England on February 4, with a knee injury.
While 2009 Test Lion Jones could follow suit after suffering serious ligament damage to his left elbow in the Ospreys defeat at London Irish.
Specialists will decide today whether to operate on the 68-cap Wales prop and he is expected to miss most if not all of the Championship.
"The news isn't great and he'll be out for a substantial period of time," said Ospreys director of coaching Scott Johnson. "It's not looking good for Wales.
"If I was a betting man I wouldn't be putting my hard earned money on him making many appearances.
"The issue is whether to operate or take a more conservative approach. He's had a scan, the decision is now in the hands of the specialists and we'll act accordingly."
The prognosis for Shanklin is clearer, the Cardiff Blues stalwart will undergo a knee operation tomorrow after suffering a recurrence of previous ligament damage.
"Unfortunately it's bad news for Tom," said Blues coach Dai Young. "He had a scan and needs an operation on his troublesome knee. He is out for three months.
"He wasn't right against Aironi and his knee was swollen afterwards. We sent him straight away for a scan and he will need an operation with a 12-week recuperation process."
Wales head coach and former Lions forwards coach Warren Gatland names his Six Nations squad on Sunday but will have several selection dilemmas after the latest set-backs.
But both regional bosses were confident Jones and Shanklin will return in time for the World Cup in New Zealand which starts this September.