Revd Steven Sizer from Christ Church in Virginia Water, Surrey allegedly posted a link to an article on the social media site which has since been removed.
Reports suggest he wrote 'Is this anti-Semitic? It raises so many questions'.
The Church of England has confirmed it's taking action. A spokesman said: "Our attention has been drawn to comments by the Revd Steven Sizer made earlier today on social media. In those comments Revd Sizer linked to an article entitled '9/11 Israel did it'.
"These comments would rightly be seen as unacceptable whenever they were posted. It is a matter of deep sorrow and shame that they have been posted in this week of all weeks.
"The Diocese of Guilford, where the Revd Sizer is licensed, is taking immediate steps to investigate. The diocese is aware of the seriousness of the matter and are also in touch with the Board of Deputies of British Jews."
This isn't the first time he's been involved in controversy over his views on Israel.
Two years ago, he reached a mediated agreement with the Board of Deputies of British Jews to end a long-running dispute over posts on his blog.