"Further prognosis of that is that he (Sean) is going to have to have a surgical repair on the shoulder. The time frame of that has probably moved him outside of six weeks," said Gibbes.
"The time frame to return to play hasn't been set in stone but it is significant enough for surgical intervention which means six to eight weeks minimum.
"It looks like that (he will miss the entire Six Nations), but they are not going to put an absolute line in the sand for him. They are just going to see how it goes."
It is very disappointing news for the Tullow man who has played only five times for Leinster this season, while he took his Ireland caps tally to 30 with three appearances during November's GUINNESS Series.
O'Brien scored his third try for Ireland in the opening win of Joe Schmidt's reign against Samoa and followed that up with starts against Australia and New Zealand.
Both O'Brien (shoulder) and fellow Leinster forward Cian Healy (ankle) will be notable absentees when Ireland get their Six Nations challenge underway against Scotland on Sunday, February 2.
The duo will also miss the final rounds of the Heineken Cup pool stages later this month - Leinster have upcoming clashes with Castres Olympique (away) and the Ospreys (home).
Gibbes added: "Of course a guy like Sean, it would be nice to have him in the team, but it is just an opportunity for other guys really and that is what we have tried to get going at Leinster in the last couple of years.
"Injuries happen, someone else gets to take their place but the same standard is expected."