While working through the EGit User Guide I ran into difficulty pushing files upstream using Eclipse Indigo SR1 (build 20110916-0149). The difficulties manifested themselves at first with an auth failed error, which was quickly resolved with a visit to Stack Overflow. But after fixing that problem I began seeing the following error while trying to push to a remote repo:

Cannot get remote repository refs.

Reason:
ssh://git@github.com:22: Passphrase for C:\Users\...\.ssh\id_rsa