Last week Gibson was confident Shillingford would get the all-clear.
''Though I felt confident about the way the two players performed at the testing, the report did not come back in our favour," said Gibson.
"Shane is obviously gutted, but Marlon's role in the team, as I have said previously, is primarily as a batsman, so the impact on him is a little bit less."
Gibson said a plan would be worked through to have the pair fully cleared for bowling in the New Year.
The 30-year-old Dominican Shillingford has had a remarkable degree of success, taking 11 wickets in the two tests in India and has snared 65 wickets in 14 tests at 32.32 apiece.
Gibson believes both will bounce back.
''They are both tough characters and have had their share of ups and downs int eh game over the years," he said.
''We have no doubt that they will emerge emerge from this latest setback with the utmost confidence."
The West Indies have a readymade replacement for Shillingford for the third test against New Zealand, starting in Hamilton Thursday in Sunil Narine.