The March security update caused Android Pay to stop working as soon as it installed on the Nexus 6. Owners of this phone started reporting it on Reddit and twitter.
Once Google got wind of it they pulled the update for the Nexus 6 and any developer sites where it was available for download. They have also disabled Android Pay for any Nexus 6 where the update was installed. This does not affect any other phones.
There is currently no ETA for when a fix will be available.