You need to allow execution of scripts from the temporary directory, or run Jenkins with a different temporary directory by creating and assigning your own value for temporary directories (like java.io.tmpdir and TMP and TEMP).

Refer to the git client plugin wiki page and its "Gotchas" section for a description of the case you're seeing.

Refer also to "Making /tmp non-executable" in the Debian documentation.

Sudin Shakya, the git client plugin 2.4.4 (released today, 27 Apr 2017) now prefers to write its temporary files into a directory near the workspace, if the workspace exists. That may help with this case, though it probably won't solve all cases, since there are times when the git plugin needs to perform an operation that requires authentication, without having a workspace available.

If git client plugin 2.4.4 does not completely resolve the issue, then you'll need to configure Jenkins to use a temporary directory where it can write scripts that are executable.

Thank you Mark. I ran the mount -o remount,exec /tmp command to give temp folder exec permissions and it works. However, I wasn't able to change the default location for the temporary directory .